Permuted Index of elprep

J
K
L
Q
X
Y
Z
                                                    %compose-filters (function)
                                     set sim-stream-%floats (function)
                                         sim-stream-%floats (function)
                                                    %make-buffer (function)
                                                    %make-split-hash-table (function)
                                                    %open-sam (function)
                                                    *cigar-consumes-reference-bases-table* (variable)
                                                    *cigar-list-cache* (variable)
                                                    *cigar-operations* (variable)
                                                    *cigar-vector-cache* (variable)
                                                    *fixnum-optimization* (variable)
                                                    *integer-types* (variable)
                                                    *keyword* (variable)
                                                    *merge-program-help* (variable)
                                                    *number-of-threads* (variable)
                                                    *optimization* (variable)
                                                    *program-help* (variable)
                                                    *program-name* (variable)
                                                    *program-url* (variable)
                                                    *program-version* (variable)
                                                    *reference-fai* (variable)
                                                    *reference-fasta* (variable)
                                                    *sam-alignment-line-output-length-factor* (variable)
                                                    *sam-file-format-date* (variable)
                                                    *sam-file-format-version* (variable)
                                                    *samtools* (variable)
                                                    *split-program-help* (variable)
                                                    *stderr* (variable)
                                                    *unique-value* (variable)
                                                    +buffer-chunk-size+ (constant)
                                                    +default-chunk-size+ (constant)
                                                    +duplicate+ (constant)
                                                    +first+ (constant)
                                                    +high-bits+ (constant)
                                                    +highest-bits+ (constant)
                                                    +last+ (constant)
                                                    +low-bits+ (constant)
                                                    +lowest-bits+ (constant)
                                                    +max-cigar-operation+ (constant)
                                                    +max-optional-field-type-tag+ (constant)
                                                    +max-upcase-cigar-operation+ (constant)
                                                    +min-cigar-operation+ (constant)
                                                    +min-optional-field-type-tag+ (constant)
                                                    +min-upcase-cigar-operation+ (constant)
                                                    +multiple+ (constant)
                                                    +next-reversed+ (constant)
                                                    +next-unmapped+ (constant)
                                                    +proper+ (constant)
                                                    +qc-failed+ (constant)
                                                    +reversed+ (constant)
                                                    +secondary+ (constant)
                                                    +supplementary+ (constant)
                                                    +total-bits+ (constant)
                                                    +unmapped+ (constant)
                                             rotate-1 (function)
                                             rotate-15 (function)
                                                    adapt-alignment (function)
                                      sam-alignment-adapted-pos (function)
                                      sam-alignment-adapted-score (function)
                                                    add-or-replace-read-group (function)
                                                    add-pg-line (function)
                                                    add-refid (function)
                                                    advance (function)
                                              adapt-alignment (function)
                                           copy-sam-alignment (function)
                                         format-sam-alignment (function)
                                           make-sam-alignment (function)
                                          parse-sam-alignment (function)
                                                sam-alignment (structure)
                                     sim-format-sam-alignment (function)
                                                sam-alignment-adapted-pos (function)
                                                sam-alignment-adapted-score (function)
                                                sam-alignment-cigar (function)
                                            set sam-alignment-cigar (function)
                                                sam-alignment-differ (function)
                                                sam-alignment-duplicate-p (function)
                                                sam-alignment-end (function)
                                               with-alignment-filters (macro)
                                                sam-alignment-first-p (function)
                                                sam-alignment-flag (function)
                                            set sam-alignment-flag (function)
                                                sam-alignment-flag-every (function)
                                                sam-alignment-flag-notany (function)
                                                sam-alignment-flag-notevery (function)
                                                sam-alignment-flag-some (function)
                                          parse-sam-alignment-from-stream (function)
                                                sam-alignment-last-p (function)
                                                sam-alignment-line (function)
                                            set sam-alignment-line (function)
                                               *sam-alignment-line-output-length-factor* (variable)
                                                sam-alignment-mapq (function)
                                            set sam-alignment-mapq (function)
                                                sam-alignment-multiple-p (function)
                                                sam-alignment-next-reversed-p (function)
                                                sam-alignment-next-unmapped-p (function)
                                       estimate-sam-alignment-output-length (function)
                                                sam-alignment-p (function)
                                                sam-alignment-pair-hash (function)
                                                sam-alignment-pair= (function)
                                                sam-alignment-pnext (function)
                                            set sam-alignment-pnext (function)
                                                sam-alignment-pos (function)
                                            set sam-alignment-pos (function)
                                                sam-alignment-proper-p (function)
                                                sam-alignment-qc-failed-p (function)
                                                sam-alignment-qname (function)
                                            set sam-alignment-qname (function)
                                                sam-alignment-qual (function)
                                            set sam-alignment-qual (function)
                                                sam-alignment-refid (function)
                                                sam-alignment-reversed-p (function)
                                                sam-alignment-rg (function)
                                                sam-alignment-rname (function)
                                            set sam-alignment-rname (function)
                                                sam-alignment-rnext (function)
                                            set sam-alignment-rnext (function)
                                                sam-alignment-same (function)
                                                sam-alignment-secondary-p (function)
                                                sam-alignment-seq (function)
                                            set sam-alignment-seq (function)
                                                sam-alignment-supplementary-p (function)
                                                sam-alignment-tag (function)
                                                sam-alignment-tags (function)
                                            set sam-alignment-tags (function)
                                                sam-alignment-temp (function)
                                                sam-alignment-temps (function)
                                            set sam-alignment-temps (function)
                                                sam-alignment-tlen (function)
                                            set sam-alignment-tlen (function)
                                                sam-alignment-unmapped-p (function)
                                                sam-alignments (function)
                                            set sam-alignments (function)
                                               pair-aln1 (function)
                                               pair-aln2 (function)
                                       command-line-arguments (function)
                                    format-sam-byte-array (function)
                                     parse-sam-byte-array (function)
                                  parse-sam-numeric-array (function)
                                sim-format-sam-byte-array (function)
                                   unwrap-displaced-array (function)
                                               mark-as-duplicate (function)
                                               with-ascii-stream-input-buffer (macro)
                                              cigar-aux-pos (function)
                                     make-unclipped-aux-tables (function)
                                          in-simple-base-string-syntax (macro)
     make-cigar-operations-table-consumes-reference-bases (function)
                             operator-consumes-read-bases-p (function)
                        operator-consumes-reference-bases-p (function)
                          *cigar-consumes-reference-bases-table* (variable)
                                                run-best-practices-pipeline (function)
                                                run-best-practices-pipeline-intermediate-list (function)
                                              +high-bits+ (constant)
                                           +highest-bits+ (constant)
                                               +low-bits+ (constant)
                                            +lowest-bits+ (constant)
                                             +total-bits+ (constant)
                                                    bounded-mailbox (structure)
                                               copy-bounded-mailbox (function)
                                               make-bounded-mailbox (function)
                                                    bounded-mailbox-mailbox (function)
                                                    bounded-mailbox-p (function)
                                                    bounded-mailbox-semaphore (function)
                                              %make-buffer (function)
                                                    buffer (structure)
                                               make-buffer (function)
                                     read-line-into-buffer (function)
                                       reinitialize-buffer (function)
                            with-ascii-stream-input-buffer (macro)
                                              write-buffer (function)
                                                    buffer-copy (function)
                                               with-buffer-dispatch (macro)
                                                    buffer-emptyp (function)
                                                    buffer-extend (function)
                                               slow-buffer-extend (function)
                                                    buffer-hash (function)
                                                    buffer-hash-value (function)
                                                    buffer-p (function)
                                                    buffer-parse-integer (function)
                                                    buffer-partition (function)
                                                    buffer-pos (function)
                                                    buffer-push (function)
                                                    buffer-str (function)
                                                    buffer-string (function)
                                                    buffer= (function)
                                          sim-write-byte (function)
                                         format-sam-byte-array (function)
                                          parse-sam-byte-array (function)
                                     sim-format-sam-byte-array (function)
                                        *cigar-list-cache* (variable)
                                      *cigar-vector-cache* (variable)
                                                    call-with-threads (function)
                                                    check-file-sorting-order (function)
                                                    check-refid-type (function)
                                                    check-stdin (function)
                                                    check-stdout (function)
                       merge-sorted-files-split-per-chromosome (function)
                     merge-unsorted-files-split-per-chromosome (function)
                                     split-file-per-chromosome (function)
                                             rename-chromosomes (function)
                                             ensure-chunk (function)
                                           with-sam-chunk (macro)
                                             create-chunk-filter (generic function)
                                               with-chunk-output (macro)
                                                    chunk-output-loop (function)
                                            +buffer-chunk-size+ (constant)
                                           +default-chunk-size+ (constant)
                               get-read-length-from-cigar (function)
                                      sam-alignment-cigar (function)
                                  set sam-alignment-cigar (function)
                                                    cigar-aux-pos (function)
                                               make-cigar-operation (function)
                                               +max-cigar-operation+ (constant)
                                        +max-upcase-cigar-operation+ (constant)
                                               +min-cigar-operation+ (constant)
                                        +min-upcase-cigar-operation+ (constant)
                                               make-cigar-operations-table (function)
                                               make-cigar-operations-table-consumes-reference-bases (function)
                                               scan-cigar-string (function)
                                          fast-scan-cigar-string-to-list (function)
                                          slow-scan-cigar-string-to-list (function)
                                          fast-scan-cigar-string-to-vector (function)
                                          slow-scan-cigar-string-to-vector (function)
                                                    classify-fragment (function)
                                                    classify-pair (function)
                                                    clean-sam (function)
                                               soft-clip-end-of-read (function)
                                  element-stradless-clipped-read (function)
                                            process-close (function)
                                                    close-sam (function)
                                         sam-header-co (function)
                                     set sam-header-co (function)
                                   parse-sam-header-code (function)
                                                    command-line-arguments (function)
                                          parse-sam-comment (function)
                                         format-sam-comments (function)
                                     sim-format-sam-comments (function)
                                                    common-number-type (function)
                                                    compare-sam-files (function)
                                                    compare-sams (function)
                                                    compose-global-filters (function)
                                                    compose-thread-filters (function)
                                                    compose-thunks (function)
                                                    compute-phred-score (function)
                                                    compute-unclipped-position (function)
                                           operator-consumes-read-bases-p (function)
                        make-cigar-operations-table-consumes-reference-bases (function)
                                           operator-consumes-reference-bases-p (function)
                                             *cigar-consumes-reference-bases-table* (variable)
                                                    coordinate< (function)
                                             buffer-copy (function)
                                                    copy-bounded-mailbox (function)
                                                    copy-handle (function)
                                                    copy-pair (function)
                                                    copy-process (function)
                                                    copy-sam (function)
                                                    copy-sam-alignment (function)
                                                    copy-sam-header (function)
                                                    copy-sim-stream (function)
                                                    copy-simple-tree (function)
                                                    copy-split-hash-table (function)
                                                    copy-stream (function)
                                                    copy-temporary-file (function)
                                                    count-duplicates (function)
                                                    create-chunk-filter (generic function)
                                                    create-log-filename (function)
                                            sorting-criterion (function)
                                   *sam-file-format-date* (variable)
                                         format-sam-datetime (function)
                                     sim-format-sam-datetime (function)
                                             elprep-debugger-hook (function)
                                                    defglobal (macro)
                                        simple-tree-depth (function)
                                  make-integer-type-descriptors (function)
                      format-sam-reference-sequence-dictionary (function)
                         replace-reference-sequence-dictionary (function)
                  sim-format-sam-reference-sequence-dictionary (function)
                       parse-sam-reference-sequence-dictionary-entry (function)
                         replace-reference-sequence-dictionary-from-sam-file (function)
                                      sam-alignment-differ (function)
                                               real-diffs (function)
                                        with-buffer-dispatch (macro)
                                             unwrap-displaced-array (function)
                                            mark-as-duplicate (function)
                                      sam-alignment-duplicate-p (function)
                                             filter-duplicate-reads (function)
                                              count-duplicates (function)
                                               mark-duplicates (function)
                                                    effective-sorting-order (function)
                                                    element-stradless-clipped-read (function)
                                                    elprep-debugger-hook (function)
                                                    elprep-filter-script (function)
                                                    elprep-merge-script (function)
                                                    elprep-script (function)
                                                    elprep-split-script (function)
                                             buffer-emptyp (function)
                                      sam-alignment-end (function)
                                                    end-of-entry-p (function)
                                          soft-clip-end-of-read (function)
                                                    ensure-chunk (function)
                                         sam-header-ensure-hd (function)
                                                    ensure-sim-space (function)
                                               slow-ensure-sim-space (function)
                                                    ensure-str (function)
            parse-sam-reference-sequence-dictionary-entry (function)
                                             end-of-entry-p (function)
                                            process-error (function)
                                               scan-error (function)
                                                    estimate-sam-alignment-output-length (function)
                                 sam-alignment-flag-every (function)
                                                    explain-flag (function)
                                             buffer-extend (function)
                                        slow-buffer-extend (function)
                  *sam-alignment-line-output-length-factor* (variable)
                                         *reference-fai* (variable)
                                                +qc-failed+ (constant)
                                   sam-alignment-qc-failed-p (function)
                                                    fast-scan-cigar-string-to-list (function)
                                                    fast-scan-cigar-string-to-vector (function)
                                         *reference-fasta* (variable)
                                      make-optional-field-scan-table (function)
                                      +max-optional-field-type-tag+ (constant)
                                      +min-optional-field-type-tag+ (constant)
                                     copy-temporary-file (function)
                                     make-temporary-file (function)
     replace-reference-sequence-dictionary-from-sam-file (function)
                                          temporary-file (structure)
                                               *sam-file-format-date* (variable)
                                               *sam-file-format-version* (variable)
                                                sam-file-kind (function)
                                          temporary-file-p (function)
                                              split-file-per-chromosome (function)
                                      set temporary-file-sibling (function)
                                          temporary-file-sibling (function)
                                              check-file-sorting-order (function)
                                         create-log-filename (function)
                                        compare-sam-files (function)
                                       merge-sorted-files-split-per-chromosome (function)
                                     merge-unsorted-files-split-per-chromosome (function)
                                       create-chunk-filter (generic function)
                                                    filter (function)
                                                    filter-duplicate-reads (function)
                                                    filter-optional-header-info (function)
                                                    filter-optional-reads (function)
                                             elprep-filter-script (function)
                                                    filter-unmapped-reads (function)
                                                    filter-unmapped-reads-strict (function)
                                                    filtermap (function)
                                           %compose-filters (function)
                                     compose-global-filters (function)
                                     compose-thread-filters (function)
                                     with-alignment-filters (macro)
                                        with-thread-filters (macro)
                                      sam-alignment-first-p (function)
                                          sim-write-fixed-size-fixnum (function)
                               sim-write-fixed-size-fixnum (function)
                                            explain-flag (function)
                                      sam-alignment-flag (function)
                                  set sam-alignment-flag (function)
                                      sam-alignment-flag-every (function)
                                      sam-alignment-flag-notany (function)
                                      sam-alignment-flag-notevery (function)
                                      sam-alignment-flag-some (function)
                                               scan-float (function)
                                          sim-write-float (function)
                                         sim-stream-floats (function)
                                          *sam-file-format-date* (variable)
                                                    format-sam (function)
                                                sim-format-sam (function)
                                                    format-sam-alignment (function)
                                                sim-format-sam-alignment (function)
                                                    format-sam-byte-array (function)
                                                sim-format-sam-byte-array (function)
                                                    format-sam-comments (function)
                                                sim-format-sam-comments (function)
                                                    format-sam-datetime (function)
                                                sim-format-sam-datetime (function)
                                                    format-sam-header (function)
                                                sim-format-sam-header (function)
                                                    format-sam-header-line (function)
                                                sim-format-sam-header-line (function)
                                                    format-sam-header-user-tag (function)
                                                sim-format-sam-header-user-tag (function)
                                                    format-sam-integer (function)
                                                sim-format-sam-integer (function)
                                                    format-sam-programs (function)
                                                sim-format-sam-programs (function)
                                                    format-sam-read-groups (function)
                                                sim-format-sam-read-groups (function)
                                                    format-sam-reference-sequence-dictionary (function)
                                                sim-format-sam-reference-sequence-dictionary (function)
                                                    format-sam-string (function)
                                                sim-format-sam-string (function)
                                                    format-sam-tag (function)
                                                sim-format-sam-tag (function)
                                                    format-sam-user-tags (function)
                                                sim-format-sam-user-tags (function)
                                          *sam-file-format-version* (variable)
                                           classify-fragment (function)
                                                    fragment-hash (function)
                                               true-fragment-p (function)
                                             handle-fragment= (function)
                                    get-read-length-from-cigar (function)
              replace-reference-sequence-dictionary-from-sam-file (function)
                                parse-sam-alignment-from-stream (function)
                                   parse-read-group-from-string (function)
                                                get-function (function)
                              split-hash-table-hash-function (function)
                                         get-output-functions (generic function)
                                        with-output-functions (macro)
                                                    get-function (function)
                                                    get-output-functions (generic function)
                                                    get-read-length-from-cigar (function)
                                                    get-samtools (function)
                                            compose-global-filters (function)
                                add-or-replace-read-group (function)
                                     parse-sam-read-group (function)
                                         parse-read-group-from-string (function)
                                    format-sam-read-groups (function)
                                sim-format-sam-read-groups (function)
                                               copy-handle (function)
                                                    handle (structure)
                                               make-handle (function)
                                                    handle-fragment= (function)
                                                    handle-hash (function)
                                                    handle-object (function)
                                                    handle-p (function)
                                                    handle-pair= (function)
                                             buffer-hash (function)
                                           fragment-hash (function)
                                             handle-hash (function)
                                               pair-hash (function)
                                 sam-alignment-pair-hash (function)
                                        with-modify-hash (macro)
                                   split-hash-table-hash-function (function)
                                        %make-split-hash-table (function)
                                         copy-split-hash-table (function)
                                 make-single-thread-hash-table (function)
                                         make-split-hash-table (function)
                                  make-synchronized-hash-table (function)
                                              split-hash-table (structure)
                                              split-hash-table-hash-function (function)
                                              split-hash-table-p (function)
                                                    hash-table-split (function)
                                              split-hash-table-vector (function)
                                             buffer-hash-value (function)
                                         set buffer-hash-value (function)
                                  sam-header-ensure-hd (function)
                                         sam-header-hd (function)
                                     set sam-header-hd (function)
                                           copy-sam-header (function)
                                         format-sam-header (function)
                                           make-sam-header (function)
                                          parse-sam-header (function)
                                                sam-header (function)
                                                sam-header (structure)
                                            set sam-header (function)
                                     sim-format-sam-header (function)
                                           skip-sam-header (function)
                                      with-prepared-header (macro)
                                                sam-header-co (function)
                                            set sam-header-co (function)
                                          parse-sam-header-code (function)
                                                sam-header-ensure-hd (function)
                                                sam-header-hd (function)
                                            set sam-header-hd (function)
                                    filter-optional-header-info (function)
                                         format-sam-header-line (function)
                                          parse-sam-header-line (function)
                                     sim-format-sam-header-line (function)
                                                sam-header-p (function)
                                                sam-header-pg (function)
                                            set sam-header-pg (function)
                                                sam-header-rg (function)
                                            set sam-header-rg (function)
                                                sam-header-sq (function)
                                            set sam-header-sq (function)
                                         format-sam-header-user-tag (function)
                                                sam-header-user-tag (function)
                                     sim-format-sam-header-user-tag (function)
                                                sam-header-user-tag-p (function)
                                                sam-header-user-tags (function)
                                            set sam-header-user-tags (function)
                                     *merge-program-help* (variable)
                                           *program-help* (variable)
                                     *split-program-help* (variable)
                                    elprep-debugger-hook (function)
                                                    in-simple-base-string-syntax (macro)
                                       run-pipeline-in-situ (generic function)
                                            scanner-index (function)
                                        set scanner-index (function)
                                     set sim-stream-index (function)
                                    set simple-tree-index (function)
                                         sim-stream-index (function)
                                        simple-tree-index (function)
                             filter-optional-header-info (function)
                                            process-input (function)
                                  with-ascii-stream-input-buffer (macro)
                                                    insert-node (function)
                                       buffer-parse-integer (function)
                                         format-sam-integer (function)
                                               scan-integer (function)
                                     sim-format-sam-integer (function)
                                          sim-write-integer (function)
                                               make-integer-type-descriptors (function)
                        run-best-practices-pipeline-intermediate-list (function)
                                                    intern-key (function)
                                                    intern-key/copy (function)
                                          read-line-into-buffer (function)
                                                    invoke-with-open-sam (function)
                                             thread-join (function)
                                       verify-order-kept (function)
                                             intern-key (function)
                                             intern-key/copy (function)
                                           sam-file-kind (function)
                                      sam-alignment-last-p (function)
                      estimate-sam-alignment-output-length (function)
                                 reference-sequence-length (function)
                         *sam-alignment-line-output-length-factor* (variable)
                                           get-read-length-from-cigar (function)
                                             add-pg-line (function)
                                  format-sam-header-line (function)
                                   parse-sam-header-line (function)
                                      sam-alignment-line (function)
                                  set sam-alignment-line (function)
                              sim-format-sam-header-line (function)
                                               skip-line (function)
                                            command-line-arguments (function)
                                               read-line-into-buffer (function)
                                     *sam-alignment-line-output-length-factor* (variable)
                          fast-scan-cigar-string-to-list (function)
           run-best-practices-pipeline-intermediate-list (function)
                          slow-scan-cigar-string-to-list (function)
                                             *cigar-list-cache* (variable)
                                             create-log-filename (function)
                                       chunk-output-loop (function)
                                            bounded-mailbox (structure)
                                    bounded-mailbox-mailbox (function)
                                       copy-bounded-mailbox (function)
                                       make-bounded-mailbox (function)
                                               make-mailbox (function)
                                            bounded-mailbox-mailbox (function)
                                            bounded-mailbox-p (function)
                                                    mailbox-read (generic function)
                                            bounded-mailbox-semaphore (function)
                                                    mailbox-send (generic function)
                                                    make-bounded-mailbox (function)
                                                    make-buffer (function)
                                                    make-cigar-operation (function)
                                                    make-cigar-operations-table (function)
                                                    make-cigar-operations-table-consumes-reference-bases (function)
                                                    make-handle (function)
                                                    make-integer-type-descriptors (function)
                                                    make-mailbox (function)
                                                    make-optional-field-scan-table (function)
                                                    make-pair (function)
                                                    make-phred-score-table (function)
                                                    make-process (function)
                                                    make-sam (function)
                                                    make-sam-alignment (function)
                                                    make-sam-header (function)
                                                    make-scanner (function)
                                                    make-sim-stream (function)
                                                    make-simple-tree (function)
                                                    make-single-thread-hash-table (function)
                                                    make-split-hash-table (function)
                                                    make-subtree (function)
                                                    make-super-tree (function)
                                                    make-synchronized-hash-table (function)
                                                    make-temporary-file (function)
                                                    make-unclipped-aux-tables (function)
                                                    mapcar* (function)
                                                    mapfilter (function)
                                                    mapfiltermap (function)
                                      sam-alignment-mapq (function)
                                  set sam-alignment-mapq (function)
                                                    mark-as-duplicate (function)
                                                    mark-duplicates (function)
                                             elprep-merge-script (function)
                                                    merge-sorted-files-split-per-chromosome (function)
                                                    merge-unsorted-files-split-per-chromosome (function)
                                               with-modify-hash (macro)
                                      sam-alignment-multiple-p (function)
                                           *program-name* (variable)
                                          sim-write-newline (function)
                                              write-newline (function)
                                      sam-alignment-next-reversed-p (function)
                                      sam-alignment-next-unmapped-p (function)
                                                    nfilter (function)
                                                    nfiltermap (function)
                                                    nmapcar* (function)
                                                    nmapfilter (function)
                                                    nmapfiltermap (function)
                                             insert-node (function)
                                        simple-tree-nodes (function)
                                 sam-alignment-flag-notany (function)
                                 sam-alignment-flag-notevery (function)
                                                    nthdiff (function)
                                             common-number-type (function)
                                          parse-sam-numeric-array (function)
                                             handle-object (function)
                                         set handle-object (function)
                                                end-of-entry-p (function)
                                      soft-clip-end-of-read (function)
                                            *number-of-threads* (variable)
                                        invoke-with-open-sam (function)
                                                    open-sam (function)
                                               with-open-sam (macro)
                                                    open-temporary-sam (function)
                                         make-cigar-operation (function)
                                         +max-cigar-operation+ (constant)
                                  +max-upcase-cigar-operation+ (constant)
                                         +min-cigar-operation+ (constant)
                                  +min-upcase-cigar-operation+ (constant)
                                             *cigar-operations* (variable)
                                         make-cigar-operations-table (function)
                                         make-cigar-operations-table-consumes-reference-bases (function)
                                                    operator-consumes-read-bases-p (function)
                                                    operator-consumes-reference-bases-p (function)
                                            *fixnum-optimization* (variable)
                                               make-optional-field-scan-table (function)
                                               +max-optional-field-type-tag+ (constant)
                                               +min-optional-field-type-tag+ (constant)
                                             filter-optional-header-info (function)
                                             filter-optional-reads (function)
                                                add-or-replace-read-group (function)
                                 check-file-sorting-order (function)
                                  effective-sorting-order (function)
                                             verify-order-kept (function)
                                            process-output (function)
                                         with-chunk-output (macro)
                                                get-output-functions (generic function)
                                               with-output-functions (macro)
                             estimate-sam-alignment-output-length (function)
                                *sam-alignment-line-output-length-factor* (variable)
                                              chunk-output-loop (function)
                                    bounded-mailbox-p (function)
                                             buffer-p (function)
                                       end-of-entry-p (function)
                                             handle-p (function)
                       operator-consumes-read-bases-p (function)
                  operator-consumes-reference-bases-p (function)
                                               pair-p (function)
                                     pair-reversed1-p (function)
                                     pair-reversed2-p (function)
                                            process-p (function)
                            sam-alignment-duplicate-p (function)
                                sam-alignment-first-p (function)
                                 sam-alignment-last-p (function)
                             sam-alignment-multiple-p (function)
                        sam-alignment-next-reversed-p (function)
                        sam-alignment-next-unmapped-p (function)
                                      sam-alignment-p (function)
                               sam-alignment-proper-p (function)
                            sam-alignment-qc-failed-p (function)
                             sam-alignment-reversed-p (function)
                            sam-alignment-secondary-p (function)
                        sam-alignment-supplementary-p (function)
                             sam-alignment-unmapped-p (function)
                                         sam-header-p (function)
                                sam-header-user-tag-p (function)
                                                sam-p (function)
                                         sim-stream-p (function)
                                        simple-tree-p (function)
                                   split-hash-table-p (function)
                                     temporary-file-p (function)
                                      true-fragment-p (function)
                                          true-pair-p (function)
                                           classify-pair (function)
                                               copy-pair (function)
                                               make-pair (function)
                                                    pair (structure)
                                                    pair-aln1 (function)
                                                    pair-aln2 (function)
                                                    pair-hash (function)
                                      sam-alignment-pair-hash (function)
                                                    pair-p (function)
                                               true-pair-p (function)
                                                    pair-pos1 (function)
                                                    pair-pos2 (function)
                                                    pair-refid1 (function)
                                                    pair-refid2 (function)
                                                    pair-reversed1-p (function)
                                                    pair-reversed2-p (function)
                                                    pair-rg (function)
                                                    pair-score (function)
                                             handle-pair= (function)
                                      sam-alignment-pair= (function)
                                             buffer-parse-integer (function)
                                                    parse-read-group-from-string (function)
                                                    parse-sam (function)
                                                    parse-sam-alignment (function)
                                                    parse-sam-alignment-from-stream (function)
                                                    parse-sam-byte-array (function)
                                                    parse-sam-comment (function)
                                                    parse-sam-header (function)
                                                    parse-sam-header-code (function)
                                                    parse-sam-header-line (function)
                                                    parse-sam-numeric-array (function)
                                                    parse-sam-program (function)
                                                    parse-sam-read-group (function)
                                                    parse-sam-reference-sequence-dictionary-entry (function)
                                                    parse-sam-tag (function)
                                             buffer-partition (function)
                                                    peekc (function)
                           merge-sorted-files-split-per-chromosome (function)
                         merge-unsorted-files-split-per-chromosome (function)
                                         split-file-per-chromosome (function)
                                         sam-header-pg (function)
                                     set sam-header-pg (function)
                                                add-pg-line (function)
                                            compute-phred-score (function)
                                               make-phred-score-table (function)
                                            process-pid (function)
                                 run-best-practices-pipeline (function)
                                                run-pipeline (generic function)
                                                run-pipeline-in-situ (generic function)
                                 run-best-practices-pipeline-intermediate-list (function)
                                      sam-alignment-pnext (function)
                                  set sam-alignment-pnext (function)
                                             buffer-pos (function)
                                          cigar-aux-pos (function)
                              sam-alignment-adapted-pos (function)
                                      sam-alignment-pos (function)
                                         set buffer-pos (function)
                                  set sam-alignment-pos (function)
                                               pair-pos1 (function)
                                               pair-pos2 (function)
                                  compute-unclipped-position (function)
                                           run-best-practices-pipeline (function)
                                           run-best-practices-pipeline-intermediate-list (function)
                                               with-prepared-header (macro)
                                                    presentp (function)
                                               copy-process (function)
                                               make-process (function)
                                                    process (structure)
                                                    process-close (function)
                                                    process-error (function)
                                                    process-input (function)
                                                    process-output (function)
                                                    process-p (function)
                                                    process-pid (function)
                                                    process-stream (function)
                                          parse-sam-program (function)
                                                run-program (function)
                                             *merge-program-help* (variable)
                                             *split-program-help* (variable)
                                         format-sam-programs (function)
                                     sim-format-sam-programs (function)
                                      sam-alignment-proper-p (function)
                                             unwind-protectn (macro)
                                             buffer-push (function)
                                      sam-alignment-qc-failed-p (function)
                                      sam-alignment-qname (function)
                                  set sam-alignment-qname (function)
                                      sam-alignment-qual (function)
                                  set sam-alignment-qual (function)
                                        simple-tree-rank (function)
                          element-stradless-clipped-read (function)
                                            mailbox-read (generic function)
                                   soft-clip-end-of-read (function)
                                  operator-consumes-read-bases-p (function)
                                     add-or-replace-read-group (function)
                                          parse-sam-read-group (function)
                                              parse-read-group-from-string (function)
                                         format-sam-read-groups (function)
                                     sim-format-sam-read-groups (function)
                                                get-read-length-from-cigar (function)
                                                    read-line-into-buffer (function)
                                                    readc (function)
                                   filter-duplicate-reads (function)
                                    filter-optional-reads (function)
                                    filter-unmapped-reads (function)
                                    filter-unmapped-reads-strict (function)
                                                    real-diffs (function)
                                               tree-reduce (function)
               make-cigar-operations-table-consumes-reference-bases (function)
                                  operator-consumes-reference-bases-p (function)
                                    *cigar-consumes-reference-bases-table* (variable)
                                         format-sam-reference-sequence-dictionary (function)
                                            replace-reference-sequence-dictionary (function)
                                     sim-format-sam-reference-sequence-dictionary (function)
                                          parse-sam-reference-sequence-dictionary-entry (function)
                                            replace-reference-sequence-dictionary-from-sam-file (function)
                                                    reference-sequence-length (function)
                                                add-refid (function)
                                      sam-alignment-refid (function)
                                              check-refid-type (function)
                                               pair-refid1 (function)
                                               pair-refid2 (function)
                                                    reinitialize-buffer (function)
                                                    reinitialize-scanner (function)
                                                    rename-chromosomes (function)
                                             add-or-replace-read-group (function)
                                                    replace-reference-sequence-dictionary (function)
                                                    replace-reference-sequence-dictionary-from-sam-file (function)
                                              +next-reversed+ (constant)
                                 sam-alignment-next-reversed-p (function)
                                      sam-alignment-reversed-p (function)
                                               pair-reversed1-p (function)
                                               pair-reversed2-p (function)
                                               pair-rg (function)
                                      sam-alignment-rg (function)
                                         sam-header-rg (function)
                                     set sam-header-rg (function)
                                      sam-alignment-rname (function)
                                  set sam-alignment-rname (function)
                                      sam-alignment-rnext (function)
                                  set sam-alignment-rnext (function)
                                                    rotate-1 (function)
                                                    rotate-15 (function)
                                             thread-run (function)
                                                    run-best-practices-pipeline (function)
                                                    run-best-practices-pipeline-intermediate-list (function)
                                                    run-pipeline (generic function)
                                                    run-pipeline-in-situ (generic function)
                                                    run-program (function)
                                              %open-sam (function)
                                              clean-sam (function)
                                              close-sam (function)
                                               copy-sam (function)
                                             format-sam (function)
                                   invoke-with-open-sam (function)
                                               make-sam (function)
                                               open-sam (function)
                                     open-temporary-sam (function)
                                              parse-sam (function)
                                                    sam (structure)
                                         sim-format-sam (function)
                                          with-open-sam (macro)
                                               copy-sam-alignment (function)
                                             format-sam-alignment (function)
                                               make-sam-alignment (function)
                                              parse-sam-alignment (function)
                                                    sam-alignment (structure)
                                         sim-format-sam-alignment (function)
                                                    sam-alignment-adapted-pos (function)
                                                    sam-alignment-adapted-score (function)
                                                    sam-alignment-cigar (function)
                                                    sam-alignment-differ (function)
                                                    sam-alignment-duplicate-p (function)
                                                    sam-alignment-end (function)
                                                    sam-alignment-first-p (function)
                                                    sam-alignment-flag (function)
                                                    sam-alignment-flag-every (function)
                                                    sam-alignment-flag-notany (function)
                                                    sam-alignment-flag-notevery (function)
                                                    sam-alignment-flag-some (function)
                                              parse-sam-alignment-from-stream (function)
                                                    sam-alignment-last-p (function)
                                                    sam-alignment-line (function)
                                                    sam-alignment-mapq (function)
                                                    sam-alignment-multiple-p (function)
                                                    sam-alignment-next-reversed-p (function)
                                                    sam-alignment-next-unmapped-p (function)
                                           estimate-sam-alignment-output-length (function)
                                                    sam-alignment-p (function)
                                                    sam-alignment-pair-hash (function)
                                                    sam-alignment-pair= (function)
                                                    sam-alignment-pnext (function)
                                                    sam-alignment-pos (function)
                                                    sam-alignment-proper-p (function)
                                                    sam-alignment-qc-failed-p (function)
                                                    sam-alignment-qname (function)
                                                    sam-alignment-qual (function)
                                                    sam-alignment-refid (function)
                                                    sam-alignment-reversed-p (function)
                                                    sam-alignment-rg (function)
                                                    sam-alignment-rname (function)
                                                    sam-alignment-rnext (function)
                                                    sam-alignment-same (function)
                                                    sam-alignment-secondary-p (function)
                                                    sam-alignment-seq (function)
                                                    sam-alignment-supplementary-p (function)
                                                    sam-alignment-tag (function)
                                                    sam-alignment-tags (function)
                                                    sam-alignment-temp (function)
                                                    sam-alignment-temps (function)
                                                    sam-alignment-tlen (function)
                                                    sam-alignment-unmapped-p (function)
                                                    sam-alignments (function)
                                             format-sam-byte-array (function)
                                              parse-sam-byte-array (function)
                                         sim-format-sam-byte-array (function)
                                               with-sam-chunk (macro)
                                              parse-sam-comment (function)
                                             format-sam-comments (function)
                                         sim-format-sam-comments (function)
                                             format-sam-datetime (function)
                                         sim-format-sam-datetime (function)
         replace-reference-sequence-dictionary-from-sam-file (function)
                                                    sam-file-kind (function)
                                            compare-sam-files (function)
                                               copy-sam-header (function)
                                             format-sam-header (function)
                                               make-sam-header (function)
                                              parse-sam-header (function)
                                                    sam-header (function)
                                                    sam-header (structure)
                                         sim-format-sam-header (function)
                                               skip-sam-header (function)
                                                    sam-header-co (function)
                                              parse-sam-header-code (function)
                                                    sam-header-ensure-hd (function)
                                                    sam-header-hd (function)
                                             format-sam-header-line (function)
                                              parse-sam-header-line (function)
                                         sim-format-sam-header-line (function)
                                                    sam-header-p (function)
                                                    sam-header-pg (function)
                                                    sam-header-rg (function)
                                                    sam-header-sq (function)
                                             format-sam-header-user-tag (function)
                                                    sam-header-user-tag (function)
                                         sim-format-sam-header-user-tag (function)
                                                    sam-header-user-tag-p (function)
                                                    sam-header-user-tags (function)
                                             format-sam-integer (function)
                                         sim-format-sam-integer (function)
                                              parse-sam-numeric-array (function)
                                                    sam-p (function)
                                              parse-sam-program (function)
                                             format-sam-programs (function)
                                         sim-format-sam-programs (function)
                                              parse-sam-read-group (function)
                                             format-sam-read-groups (function)
                                         sim-format-sam-read-groups (function)
                                             format-sam-reference-sequence-dictionary (function)
                                         sim-format-sam-reference-sequence-dictionary (function)
                                              parse-sam-reference-sequence-dictionary-entry (function)
                                             format-sam-string (function)
                                         sim-format-sam-string (function)
                                             format-sam-tag (function)
                                              parse-sam-tag (function)
                                         sim-format-sam-tag (function)
                                             format-sam-user-tags (function)
                                         sim-format-sam-user-tags (function)
                                      sam-alignment-same (function)
                                            compare-sams (function)
                                                get-samtools (function)
                                                    scan-cigar-string (function)
                                               fast-scan-cigar-string-to-list (function)
                                               slow-scan-cigar-string-to-list (function)
                                               fast-scan-cigar-string-to-vector (function)
                                               slow-scan-cigar-string-to-vector (function)
                                                    scan-error (function)
                                                    scan-float (function)
                                                    scan-integer (function)
                                                    scan-string (function)
                                make-optional-field-scan-table (function)
                                                    scanc (function)
                                               make-scanner (function)
                                       reinitialize-scanner (function)
                                                    scanner (structure)
                                                    scanner-index (function)
                                                    scanner-string (function)
                                      compute-phred-score (function)
                                               pair-score (function)
                              sam-alignment-adapted-score (function)
                                         make-phred-score-table (function)
                                      elprep-filter-script (function)
                                       elprep-merge-script (function)
                                             elprep-script (function)
                                       elprep-split-script (function)
                                      sam-alignment-secondary-p (function)
                                    bounded-mailbox-semaphore (function)
                                            mailbox-send (generic function)
                                      sam-alignment-seq (function)
                                  set sam-alignment-seq (function)
                               format-sam-reference-sequence-dictionary (function)
                                  replace-reference-sequence-dictionary (function)
                           sim-format-sam-reference-sequence-dictionary (function)
                                parse-sam-reference-sequence-dictionary-entry (function)
                                  replace-reference-sequence-dictionary-from-sam-file (function)
                                          reference-sequence-length (function)
                                                    set buffer-hash-value (function)
                                                    set buffer-pos (function)
                                                    set buffer-str (function)
                                                    set handle-object (function)
                                                    set sam-alignment-cigar (function)
                                                    set sam-alignment-flag (function)
                                                    set sam-alignment-line (function)
                                                    set sam-alignment-mapq (function)
                                                    set sam-alignment-pnext (function)
                                                    set sam-alignment-pos (function)
                                                    set sam-alignment-qname (function)
                                                    set sam-alignment-qual (function)
                                                    set sam-alignment-rname (function)
                                                    set sam-alignment-rnext (function)
                                                    set sam-alignment-seq (function)
                                                    set sam-alignment-tags (function)
                                                    set sam-alignment-temps (function)
                                                    set sam-alignment-tlen (function)
                                                    set sam-alignments (function)
                                                    set sam-header (function)
                                                    set sam-header-co (function)
                                                    set sam-header-hd (function)
                                                    set sam-header-pg (function)
                                                    set sam-header-rg (function)
                                                    set sam-header-sq (function)
                                                    set sam-header-user-tags (function)
                                                    set scanner-index (function)
                                                    set scanner-string (function)
                                                    set sim-stream-%floats (function)
                                                    set sim-stream-index (function)
                                                    set sim-stream-string (function)
                                                    set simple-tree-index (function)
                                                    set temporary-file-sibling (function)
                                                    setup-standard-streams (function)
                                 set temporary-file-sibling (function)
                                     temporary-file-sibling (function)
                                                    sim-format-sam (function)
                                                    sim-format-sam-alignment (function)
                                                    sim-format-sam-byte-array (function)
                                                    sim-format-sam-comments (function)
                                                    sim-format-sam-datetime (function)
                                                    sim-format-sam-header (function)
                                                    sim-format-sam-header-line (function)
                                                    sim-format-sam-header-user-tag (function)
                                                    sim-format-sam-integer (function)
                                                    sim-format-sam-programs (function)
                                                    sim-format-sam-read-groups (function)
                                                    sim-format-sam-reference-sequence-dictionary (function)
                                                    sim-format-sam-string (function)
                                                    sim-format-sam-tag (function)
                                                    sim-format-sam-user-tags (function)
                                             ensure-sim-space (function)
                                        slow-ensure-sim-space (function)
                                               copy-sim-stream (function)
                                               make-sim-stream (function)
                                                    sim-stream (structure)
                                                    sim-stream-%floats (function)
                                                    sim-stream-floats (function)
                                                    sim-stream-index (function)
                                                    sim-stream-p (function)
                                                    sim-stream-string (function)
                                                    sim-write-byte (function)
                                                    sim-write-fixed-size-fixnum (function)
                                                    sim-write-float (function)
                                                    sim-write-integer (function)
                                                    sim-write-newline (function)
                                                    sim-write-tab (function)
                                                    sim-writec (function)
                                                    sim-writestr (function)
                                                 in-simple-base-string-syntax (macro)
                                               copy-simple-tree (function)
                                               make-simple-tree (function)
                                                    simple-tree (structure)
                                                    simple-tree-depth (function)
                                                    simple-tree-index (function)
                                                    simple-tree-nodes (function)
                                                    simple-tree-p (function)
                                                    simple-tree-rank (function)
                                               make-single-thread-hash-table (function)
                                    run-pipeline-in-situ (generic function)
                                      +buffer-chunk-size+ (constant)
                                     +default-chunk-size+ (constant)
                                    sim-write-fixed-size-fixnum (function)
                                                    skip-line (function)
                                                    skip-sam-header (function)
                                                    slow-buffer-extend (function)
                                                    slow-ensure-sim-space (function)
                                                    slow-scan-cigar-string-to-list (function)
                                                    slow-scan-cigar-string-to-vector (function)
                                                    soft-clip-end-of-read (function)
                                 sam-alignment-flag-some (function)
                                              merge-sorted-files-split-per-chromosome (function)
                                                    sorting-criterion (function)
                                         check-file-sorting-order (function)
                                          effective-sorting-order (function)
                                         ensure-sim-space (function)
                                    slow-ensure-sim-space (function)
                                         hash-table-split (function)
                                                    split-file-per-chromosome (function)
                                              %make-split-hash-table (function)
                                               copy-split-hash-table (function)
                                               make-split-hash-table (function)
                                                    split-hash-table (structure)
                                                    split-hash-table-hash-function (function)
                                                    split-hash-table-p (function)
                                                    split-hash-table-vector (function)
                                 merge-sorted-files-split-per-chromosome (function)
                               merge-unsorted-files-split-per-chromosome (function)
                                             elprep-split-script (function)
                                         sam-header-sq (function)
                                     set sam-header-sq (function)
                                              setup-standard-streams (function)
                                              check-stdin (function)
                                              check-stdout (function)
                                             buffer-str (function)
                                             ensure-str (function)
                                         set buffer-str (function)
                                            element-stradless-clipped-read (function)
                                           copy-sim-stream (function)
                                               copy-stream (function)
                                           make-sim-stream (function)
                           parse-sam-alignment-from-stream (function)
                                            process-stream (function)
                                                sim-stream (structure)
                                            set sim-stream-%floats (function)
                                                sim-stream-%floats (function)
                                                sim-stream-floats (function)
                                            set sim-stream-index (function)
                                                sim-stream-index (function)
                                         with-ascii-stream-input-buffer (macro)
                                                sim-stream-p (function)
                                            set sim-stream-string (function)
                                                sim-stream-string (function)
                                     setup-standard-streams (function)
                              filter-unmapped-reads-strict (function)
                                             buffer-string (function)
                                         format-sam-string (function)
                              parse-read-group-from-string (function)
                                         scan-cigar-string (function)
                                               scan-string (function)
                                            scanner-string (function)
                                        set scanner-string (function)
                                     set sim-stream-string (function)
                                     sim-format-sam-string (function)
                                         sim-stream-string (function)
                                     in-simple-base-string-syntax (macro)
                                    fast-scan-cigar-string-to-list (function)
                                    slow-scan-cigar-string-to-list (function)
                                    fast-scan-cigar-string-to-vector (function)
                                    slow-scan-cigar-string-to-vector (function)
                                               make-subtree (function)
                                               make-super-tree (function)
                                      sam-alignment-supplementary-p (function)
                                               make-synchronized-hash-table (function)
                              in-simple-base-string-syntax (macro)
                                          sim-write-tab (function)
                                              write-tab (function)
                                   %make-split-hash-table (function)
                                    copy-split-hash-table (function)
                              make-cigar-operations-table (function)
                           make-optional-field-scan-table (function)
                                   make-phred-score-table (function)
                            make-single-thread-hash-table (function)
                                    make-split-hash-table (function)
                             make-synchronized-hash-table (function)
                                         split-hash-table (structure)
                    *cigar-consumes-reference-bases-table* (variable)
                              make-cigar-operations-table-consumes-reference-bases (function)
                                         split-hash-table-hash-function (function)
                                         split-hash-table-p (function)
                                               hash-table-split (function)
                                         split-hash-table-vector (function)
                                 make-unclipped-aux-tables (function)
                             format-sam-header-user-tag (function)
                                         format-sam-tag (function)
                                          parse-sam-tag (function)
                                      sam-alignment-tag (function)
                                    sam-header-user-tag (function)
                         sim-format-sam-header-user-tag (function)
                                     sim-format-sam-tag (function)
                           +max-optional-field-type-tag+ (constant)
                           +min-optional-field-type-tag+ (constant)
                                    sam-header-user-tag-p (function)
                                    format-sam-user-tags (function)
                                      sam-alignment-tags (function)
                                    sam-header-user-tags (function)
                                  set sam-alignment-tags (function)
                                set sam-header-user-tags (function)
                                sim-format-sam-user-tags (function)
                                      sam-alignment-temp (function)
                                               copy-temporary-file (function)
                                               make-temporary-file (function)
                                                    temporary-file (structure)
                                                    temporary-file-p (function)
                                                    temporary-file-sibling (function)
                                               open-temporary-sam (function)
                                      sam-alignment-temps (function)
                                  set sam-alignment-temps (function)
                                            compose-thread-filters (function)
                                               with-thread-filters (macro)
                                        make-single-thread-hash-table (function)
                                                    thread-join (function)
                                                    thread-run (function)
                                          call-with-threads (function)
                                         *number-of-threads* (variable)
                                            compose-thunks (function)
                                      sam-alignment-tlen (function)
                                  set sam-alignment-tlen (function)
                             fast-scan-cigar-string-to-list (function)
                             slow-scan-cigar-string-to-list (function)
                             fast-scan-cigar-string-to-vector (function)
                             slow-scan-cigar-string-to-vector (function)
                                        copy-simple-tree (function)
                                        make-simple-tree (function)
                                         make-super-tree (function)
                                             simple-tree (structure)
                                             simple-tree-depth (function)
                                         set simple-tree-index (function)
                                             simple-tree-index (function)
                                             simple-tree-nodes (function)
                                             simple-tree-p (function)
                                             simple-tree-rank (function)
                                                    tree-reduce (function)
                                                    true-fragment-p (function)
                                                    true-pair-p (function)
                                        check-refid-type (function)
                                      common-number-type (function)
                                       make-integer-type-descriptors (function)
                                +max-optional-field-type-tag+ (constant)
                                +min-optional-field-type-tag+ (constant)
                                           *integer-types* (variable)
                                               make-unclipped-aux-tables (function)
                                            compute-unclipped-position (function)
                                                    unique (function)
                                              +next-unmapped+ (constant)
                                 sam-alignment-next-unmapped-p (function)
                                      sam-alignment-unmapped-p (function)
                                             filter-unmapped-reads (function)
                                             filter-unmapped-reads-strict (function)
                                              merge-unsorted-files-split-per-chromosome (function)
                                                    unwind-protectn (macro)
                                                    unwrap-displaced-array (function)
                                               +max-upcase-cigar-operation+ (constant)
                                               +min-upcase-cigar-operation+ (constant)
                                           *program-url* (variable)
                                  format-sam-header-user-tag (function)
                                         sam-header-user-tag (function)
                              sim-format-sam-header-user-tag (function)
                                         sam-header-user-tag-p (function)
                                         format-sam-user-tags (function)
                                         sam-header-user-tags (function)
                                     set sam-header-user-tags (function)
                                     sim-format-sam-user-tags (function)
                                        buffer-hash-value (function)
                                    set buffer-hash-value (function)
                                            *unique-value* (variable)
                          fast-scan-cigar-string-to-vector (function)
                          slow-scan-cigar-string-to-vector (function)
                                   split-hash-table-vector (function)
                                             *cigar-vector-cache* (variable)
                                                    verify-order-kept (function)
                                           *program-version* (variable)
                                   *sam-file-format-version* (variable)
                                                    with-alignment-filters (macro)
                                                    with-ascii-stream-input-buffer (macro)
                                                    with-buffer-dispatch (macro)
                                                    with-chunk-output (macro)
                                                    with-modify-hash (macro)
                                             invoke-with-open-sam (function)
                                                    with-open-sam (macro)
                                                    with-output-functions (macro)
                                                    with-prepared-header (macro)
                                                    with-sam-chunk (macro)
                                                    with-thread-filters (macro)
                                               call-with-threads (function)
                                                    write-buffer (function)
                                                sim-write-byte (function)
                                                sim-write-fixed-size-fixnum (function)
                                                sim-write-float (function)
                                                sim-write-integer (function)
                                                sim-write-newline (function)
                                                    write-newline (function)
                                                sim-write-tab (function)
                                                    write-tab (function)
                                                sim-writec (function)
                                                    writec (function)
                                                    writeln (function)
                                                sim-writestr (function)
                                                    writestr (function)