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github.com/arq5x/bedtools2
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Functions
2,929 in github.com/arq5x/bedtools2
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Functions
2,929
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Types & classes
454
↓ 1 callers
Function
hts_tpool_add_result
* Adds a result to the end of the process result queue. * * Returns 0 on success; * -1 on failure */
src/utils/htslib/thread_pool.c:81
↓ 1 callers
Function
hts_tpool_process_attach
* Attach and detach a thread process-queue with / from the thread pool * scheduler. * * We need to do attach after making a thread process, but may
src/utils/htslib/thread_pool.c:416
↓ 1 callers
Function
hts_tpool_process_detach
src/utils/htslib/thread_pool.c:432
↓ 1 callers
Function
hts_tpool_process_len
* Returns the number of completed jobs in the process results queue. */
src/utils/htslib/thread_pool.c:271
↓ 1 callers
Function
hts_tpool_process_qsize
Returns the process queue size */
src/utils/htslib/thread_pool.c:918
↓ 1 callers
Function
hts_tpool_process_ref_decr
src/utils/htslib/thread_pool.c:256
↓ 1 callers
Function
hts_tpool_process_ref_incr
src/utils/htslib/thread_pool.c:250
↓ 1 callers
Function
hts_tpool_process_shutdown
* Shutdown a process. * * This sets the shutdown flag and wakes any threads waiting on process * condition variables. */
src/utils/htslib/thread_pool.c:301
↓ 1 callers
Function
hts_tpool_process_sz
* Returns the number of completed jobs in the process results queue plus the * number running and queued up to run. */
src/utils/htslib/thread_pool.c:285
↓ 1 callers
Function
hts_utell
src/utils/htslib/hts.c:1128
↓ 1 callers
Function
http_status_errno
src/utils/htslib/hfile_libcurl.c:116
↓ 1 callers
Function
hypergeo
hypergeometric distribution
src/utils/htslib/kfunc.c:207
↓ 1 callers
Function
hypergeo
hypergeometric distribution
src/fisher/kfunc.cpp:180
↓ 1 callers
Function
idx_format_name
src/utils/htslib/hts.c:1327
↓ 1 callers
Method
ignoreCase
src/utils/Contexts/ContextGroupBy.h:22
↓ 1 callers
Method
ignoreDownstream
src/utils/Contexts/ContextClosest.h:25
↓ 1 callers
Method
ignoreOverlaps
src/utils/Contexts/ContextClosest.h:23
↓ 1 callers
Method
ignoreUpstream
src/utils/Contexts/ContextClosest.h:24
↓ 1 callers
Function
inflate_block
Inflate the block in fp->compressed_block into fp->uncompressed_block
src/utils/htslib/bgzf.c:579
↓ 1 callers
Method
init
src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp:67
↓ 1 callers
Method
init
src/regressTest/RegressTest.cpp:41
↓ 1 callers
Method
init
src/fisher/fisher.cpp:22
↓ 1 callers
Method
initFromFile
src/utils/FileRecordTools/Records/VcfRecord.cpp:11
↓ 1 callers
Function
init_filters
src/utils/htslib/synced_bcf_reader.c:115
↓ 1 callers
Function
insert_to_l
src/utils/htslib/hts.c:1364
↓ 1 callers
Function
int32_get_blk
As int32_decoded/encode, but from/to blocks instead of cram_fd */
src/utils/htslib/cram/cram_io.c:511
↓ 1 callers
Function
int32_put_blk
As int32_decoded/encode, but from/to blocks instead of cram_fd */
src/utils/htslib/cram/cram_io.c:525
↓ 1 callers
Function
int64tostr
MinGW's printf has problem with "%lld" */
src/utils/htslib/knetfile.c:121
↓ 1 callers
Function
intersect_help
src/intersectFile/intersectHelp.cpp:15
↓ 1 callers
Method
intersects
src/utils/NewChromsweep/NewChromsweep.cpp:303
↓ 1 callers
Method
isBam
src/utils/FileRecordTools/FileReaders/InputStreamMgr.h:37
↓ 1 callers
Method
isCompressed
src/utils/FileRecordTools/FileReaders/InputStreamMgr.h:40
↓ 1 callers
Method
isCram
src/utils/FileRecordTools/FileRecordMgr.h:111
↓ 1 callers
Method
isCram
src/utils/FileRecordTools/FileReaders/InputStreamMgr.h:38
↓ 1 callers
Method
isGzipped
src/utils/FileRecordTools/FileReaders/InputStreamMgr.h:35
↓ 1 callers
Method
isOpen
src/utils/FileRecordTools/FileReaders/BamFileReader.cpp:24
↓ 1 callers
Function
is_dns_compliant
src/utils/htslib/hfile_s3.c:125
↓ 1 callers
Function
is_escaped
src/utils/htslib/vcf.c:281
↓ 1 callers
Function
isalpha_c
src/utils/htslib/textutils_internal.h:161
↓ 1 callers
Function
islower_c
src/utils/htslib/textutils_internal.h:164
↓ 1 callers
Function
isprint_c
src/utils/htslib/textutils_internal.h:165
↓ 1 callers
Function
jaccard_help
src/jaccard/jaccardHelp.cpp:14
↓ 1 callers
Function
kbs_init2
Initialise a bit set capable of holding ni integers, 0 <= i < ni. The set returned is empty if fill == 0, or all of [0,ni) otherwise.
src/utils/htslib/htslib/kbitset.h:70
↓ 1 callers
Function
kbs_logical_and
Logical AND
src/utils/htslib/bcf_sr_sort.c:55
↓ 1 callers
Function
kf_betai
src/utils/htslib/kfunc.c:174
↓ 1 callers
Function
kf_betai
src/fisher/kfunc.cpp:147
↓ 1 callers
Function
kf_erfc
complementary error function * \frac{2}{\sqrt{\pi}} \int_x^{\infty} e^{-t^2} dt * AS66, 2nd algorithm, http://lib.stat.cmu.edu/apstat/66 */
src/utils/htslib/kfunc.c:56
↓ 1 callers
Function
kf_erfc
complementary error function * \frac{2}{\sqrt{\pi}} \int_x^{\infty} e^{-t^2} dt * AS66, 2nd algorithm, http://lib.stat.cmu.edu/apstat/66 */
src/fisher/kfunc.cpp:29
↓ 1 callers
Function
kf_gammaq
src/utils/htslib/kfunc.c:138
↓ 1 callers
Function
kf_gammaq
src/fisher/kfunc.cpp:111
↓ 1 callers
Function
kftp_parse_url
initialize ->type, ->host, ->retr and ->size
src/utils/htslib/knetfile.c:303
↓ 1 callers
Function
kftp_pasv_connect
src/utils/htslib/knetfile.c:266
↓ 1 callers
Function
kftp_pasv_prep
src/utils/htslib/knetfile.c:251
↓ 1 callers
Function
kftp_reconnect
src/utils/htslib/knetfile.c:291
↓ 1 callers
Function
kget_int64
src/utils/htslib/cram/cram_index.c:110
↓ 1 callers
Function
khttp_parse_url
src/utils/htslib/knetfile.c:379
↓ 1 callers
Function
knet_win32_destroy
src/utils/htslib/knetfile.c:149
↓ 1 callers
Function
ksBM_prep
reference: http://www-igm.univ-mlv.fr/~lecroq/string/node14.html
src/utils/htslib/kstring.c:281
↓ 1 callers
Function
ksplit
* Returns 's' split by delimiter, with *n being the number of components; * NULL on failue. */
src/utils/htslib/htslib/kstring.h:234
↓ 1 callers
Function
ksplit_core
s MUST BE a null terminated string; l = strlen(s)
src/utils/htslib/kstring.c:205
↓ 1 callers
Function
kstrstr
src/utils/htslib/kstring.c:342
↓ 1 callers
Function
kt_fisher_exact
src/fisher/kfunc.cpp:212
↓ 1 callers
Function
kvsprintf
src/utils/htslib/kstring.c:141
↓ 1 callers
Function
le_int2
src/utils/htslib/cram/os.h:157
↓ 1 callers
Function
links_main
src/linksBed/linksMain.cpp:27
↓ 1 callers
Method
loadBedCovListFileIntoMap
src/utils/bedFile/bedFile.cpp:720
↓ 1 callers
Method
loadBedFileIntoMergedMap
src/utils/bedFile/bedFile.cpp:674
↓ 1 callers
Method
loadBedFileIntoVector
src/utils/bedFile/bedFile.cpp:768
↓ 1 callers
Method
loadBedPEFileIntoMap
src/utils/bedFilePE/bedFilePE.cpp:470
↓ 1 callers
Method
loadDB
src/utils/BinTree/BinTree.cpp:12
↓ 1 callers
Function
load_hfile_plugins
src/utils/htslib/hfile.c:1016
↓ 1 callers
Method
load_index
src/utils/BamTools/include/BamReader.hpp:53
↓ 1 callers
Function
load_plugin
src/utils/htslib/plugin.c:135
↓ 1 callers
Function
logbinomial_table
generates a success * trials table of bionomial probability densities (log transformed) */
src/utils/htslib/errmod.c:50
↓ 1 callers
Function
lossy_read_names
* Lossily reject read names. * * The rule here is that if all reads for this template reside in the * same slice then we can lose the name. Otherw
src/utils/htslib/cram/cram_encode.c:1129
↓ 1 callers
Function
lzma_mem_deflate
src/utils/htslib/cram/cram_io.c:675
↓ 1 callers
Function
lzma_mem_inflate
src/utils/htslib/cram/cram_io.c:693
↓ 1 callers
Function
main
()
scripts/makeBashScripts.py:11
↓ 1 callers
Method
main
src/split/splitBed.cpp:75
↓ 1 callers
Function
map_help
src/mapFile/mapHelp.cpp:11
↓ 1 callers
Function
maskfastafrombed_main
src/maskFastaFromBed/maskFastaFromBedMain.cpp:27
↓ 1 callers
Function
merge_help
src/mergeFile/mergeHelp.cpp:16
↓ 1 callers
Function
merge_vsets
src/utils/htslib/bcf_sr_sort.c:220
↓ 1 callers
Function
mfclose
* Closes an mFILE. If the filename is known (implying write access) then this * also writes the data to disk. * * Stdout is handled by calling mffl
src/utils/htslib/cram/mFILE.c:348
↓ 1 callers
Function
mfdetach
* Closes the file pointer contained within the mFILE without destroying * the in-memory data. * * Attempting to do this on an mmaped buffer is an e
src/utils/htslib/cram/mFILE.c:376
↓ 1 callers
Function
mfmmap
* mmaps in the file, but only for reading currently. * * Returns 0 on success * -1 on failure */
src/utils/htslib/cram/mFILE.c:118
↓ 1 callers
Function
mfopen
* Opens a file. If we have read access (r or a+) then it loads the entire * file into memory. If We have write access then the pathname is stored. *
src/utils/htslib/cram/mFILE.c:334
↓ 1 callers
Function
mfsteal
src/utils/htslib/cram/mFILE.c:415
↓ 1 callers
Function
mfwrite
src/utils/htslib/cram/mFILE.c:514
↓ 1 callers
Function
mkdir_prefix
* Make the directory containing path and any prefix directories. */
src/utils/htslib/cram/cram_io.c:1977
↓ 1 callers
Function
mode2level
get the compress level from the mode string: compress_level==-1 for the default level, -2 plain uncompressed
src/utils/htslib/bgzf.c:243
↓ 1 callers
Function
mp_destroy
src/utils/htslib/sam.c:2238
↓ 1 callers
Function
mp_init
src/utils/htslib/sam.c:2232
↓ 1 callers
Function
mrewind
src/utils/htslib/cram/mFILE.c:462
↓ 1 callers
Function
mt_flush_queue
src/utils/htslib/bgzf.c:1486
↓ 1 callers
Function
multi_is_exact
src/utils/htslib/bcf_sr_sort.c:117
↓ 1 callers
Function
multi_is_subset
src/utils/htslib/bcf_sr_sort.c:145
↓ 1 callers
Function
multibamcov_main
src/multiBamCov/multiBamCovMain.cpp:27
↓ 1 callers
Function
multiintersect_examples
src/multiIntersectBed/multiIntersectBedMain.cpp:204
↓ 1 callers
Function
multiintersect_main
src/multiIntersectBed/multiIntersectBedMain.cpp:43
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