%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)