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