%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)