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Searched refs:readlength (Results 1 – 25 of 51) sorted by relevance

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/dports/biology/gmap/gmap-2020-09-12/src/
H A Dsamread.c38 int readlength; in cigar_string_readlength() local
47 readlength = 0; in cigar_string_readlength()
67 readlength += (int) npos; in cigar_string_readlength()
75 readlength += (int) npos; in cigar_string_readlength()
90 return readlength; in cigar_string_readlength()
1166 if (*readlength == 0) {
1266 if (*readlength == 0) { in Samread_parse_read_fromfile()
1580 *readlength = 0;
1607 *readlength += npos;
1609 *readlength += npos;
[all …]
H A Dsam_sort.c855 int acclength, last_acclength, readlength; in process_with_dups() local
988 make_complement_inplace(read,readlength); in process_with_dups()
1002 make_complement_inplace(read,readlength); in process_with_dups()
1013 make_complement_inplace(read,readlength); in process_with_dups()
1026 make_complement_inplace(read,readlength); in process_with_dups()
1086 make_complement_inplace(read,readlength); in process_with_dups()
1099 make_complement_inplace(read,readlength); in process_with_dups()
1168 make_complement_inplace(read,readlength); in process_with_dups()
1177 make_complement_inplace(read,readlength); in process_with_dups()
1188 make_complement_inplace(read,readlength); in process_with_dups()
[all …]
H A Dsamread.h28 Samread_parse_read_fromfile (FILE *fp, unsigned int *flag, int *readlength, char **read, int linele…
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/
H A DJunctionTreeKBestHaplotypeFinderUnitTest.java79 final int readlength = 6; in testDegenerateLoopingCase() local
316 int readlength = 20; in testPerfectlyPhasedHaplotypeRecoveryRef() local
351 int readlength = 20; in testInsufficientJunctionTreeDataCausingCombinatorialExpansion() local
387 int readlength = 20; in testPerfectlyPhasedHaplotypeRecoveryTwoAlts() local
423 int readlength = 15; in testNonUniqueRefStopPosition() local
456 int readlength = 15; in testNonUniqueRefStopPositionNoStopJTToResolveIt() local
489 int readlength = 15; in testReferenceEndWithErrorSpanningPastEndBase() local
523 int readlength = 15; in testFullReferencePathRecoveryDespiteReadsNotReachingLastBase() local
557 int readlength = 15; in testOfLoopingReferenceReadsTooShortToRecoverIt() local
1206 int readlength = 20; in testCreateMapOfPivotalEdgesInTopoglogicalOrderBasicExample() local
[all …]
/dports/biology/velvet/velvet_1.2.10/contrib/afg_handling/
H A Dsnp_view.pl48 my $readlength = 50;
58 my $low = $posn - $readlength;
59 my $high = $posn + $readlength;
122 my $num_spaces = 2 * $readlength - length($low) -1;
124 if($i == $readlength-length($low)){
/dports/net-p2p/btcheck/btcheck-2.1/src/
H A Dcheck.c35 integer_t readlength; in check() local
86 readlength = 0; in check()
87 while (readlength < torrentinfolength) { in check()
88 length = MIN(torrentinfopiecelength, torrentinfolength-readlength); in check()
110 readlength += length; in check()
/dports/comms/owfs/owfs-3.2p4/module/owlib/src/include/
H A Dow_transaction.h134 #define TRXN_WR_CRC16(pointer,writelength,readlength) \ argument
136 TRXN_READ(((BYTE *)pointer)+(writelength),readlength+2), \
137 TRXN_CRC16((BYTE *)pointer,writelength+readlength+2)
139 #define TRXN_WR_CRC16_SEEDED(pointer,seed, writelength,readlength) \ argument
141 TRXN_READ(((BYTE *)pointer)+(writelength),readlength+2), \
142 TRXN_CRC16_seeded((BYTE *)pointer, writelength+readlength+2, (BYTE *) (seed) )
/dports/www/chromium-legacy/chromium-88.0.4324.182/third_party/pdfium/core/fxcodec/jpx/
H A Djpx_decode_utils.cpp28 OPJ_SIZE_T readlength = nb_bytes < bufferLength ? nb_bytes : bufferLength; in opj_read_from_memory() local
29 memcpy(p_buffer, &srcData->src_data[srcData->offset], readlength); in opj_read_from_memory()
30 srcData->offset += readlength; in opj_read_from_memory()
31 return readlength; in opj_read_from_memory()
/dports/www/qt5-webengine/qtwebengine-everywhere-src-5.15.2/src/3rdparty/chromium/third_party/pdfium/core/fxcodec/jpx/
H A Djpx_decode_utils.cpp28 OPJ_SIZE_T readlength = nb_bytes < bufferLength ? nb_bytes : bufferLength; in opj_read_from_memory() local
29 memcpy(p_buffer, &srcData->src_data[srcData->offset], readlength); in opj_read_from_memory()
30 srcData->offset += readlength; in opj_read_from_memory()
31 return readlength; in opj_read_from_memory()
/dports/devel/py-defusedxml/defusedxml-0.6.0/defusedxml/
H A Dxmlrpc.py83 self.readlength = None
86 self.readlength = 0
94 left = self.limit - self.readlength
97 self.readlength += len(data)
98 if self.readlength > self.limit:
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/pileup/
H A DReadPileupUnitTest.java311 final int readlength = 10; in testSimplePileup() local
312 final byte[] bases1 = Utils.repeatChars('A', readlength); in testSimplePileup()
316 final byte[] bases2 = Utils.repeatChars('C', readlength); in testSimplePileup()
360 final int readlength = 10; in testSimplePileupWithIndelsOffset() local
361 final byte[] bases1 = Utils.repeatChars('A', readlength); in testSimplePileupWithIndelsOffset()
365 final byte[] bases2 = Utils.repeatChars('C', readlength); in testSimplePileupWithIndelsOffset()
418 final int readlength = 10; in testSimplePileupWithOffset() local
419 final byte[] bases1 = Utils.repeatChars('A', readlength); in testSimplePileupWithOffset()
423 final byte[] bases2 = Utils.repeatChars('C', readlength); in testSimplePileupWithOffset()
633 final int readlength = 10; in testOverlappingFragmentFilter() local
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/dports/science/nwchem-data/nwchem-7.0.2-release/src/lucia/
H A Dcio.c153 INT readlength; local
156 readlength = MIN(bfrblk,remains);
157 rc = (INT)read(*FileDescriptor,(void *)(Buffer+i),(size_t)(readlength));
158 if ( rc == readlength ) { i = i+readlength; rc = i; remains = remains - bfrblk;}
/dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/lucia/
H A Dcio.c153 INT readlength; local
156 readlength = MIN(bfrblk,remains);
157 rc = (INT)read(*FileDescriptor,(void *)(Buffer+i),(size_t)(readlength));
158 if ( rc == readlength ) { i = i+readlength; rc = i; remains = remains - bfrblk;}
/dports/net/pear-File_Bittorrent2/File_Bittorrent2-1.3.1/File/Bittorrent2/
H A DMakeTorrent.php335 $readlength = 8192;
337 $readlength = $this->piece_length - $datalength;
340 $tmpdata = fread($this->fp, $readlength);
/dports/graphics/exifprobe/exifprobe-2.0.1/
H A Dprint.c2375 unsigned long remaining,readlength; in hexdump() local
2384 readlength = MAXBUFLEN; in hexdump()
2386 readlength = size; in hexdump()
2390 if(size > readlength) in hexdump()
2391 readlength = (readlength / width) * width; in hexdump()
2410 if(max_to_print < readlength) in hexdump()
2412 readlength = max_to_print; in hexdump()
2417 while(bytes < readlength) in hexdump()
2420 remaining = readlength - bytes; in hexdump()
2440 remaining = readlength - bytes; in hexdump()
[all …]
/dports/biology/bbmap/bbmap/current/jgi/
H A DSynthMDA.java97 readlength=Integer.parseInt(b); in SynthMDA()
262 list.add("length="+readlength); in process()
394 private int readlength=150; field in SynthMDA
/dports/security/shibboleth-sp/shibboleth-sp-3.3.0/shibsp/remoting/impl/
H A DSocketListener.cpp528 int readlength = m_listener->recv(m_sock,(char*)&len,sizeof(len)); in job() local
529 if (readlength == 0) { in job()
533 else if (readlength != sizeof(len)) { in job()
/dports/www/ilias/ILIAS-5.4.25/libs/composer/vendor/james-heinrich/getid3/getid3/
H A Dmodule.audio.ogg.php649 $readlength = self::OggPageSegmentLength($info['ogg']['pageheader'][$VorbisCommentPage], 1);
650 if ($readlength <= 0) {
654 $commentdata .= $this->fread($readlength);
/dports/chinese/wordpress-zh_CN/wordpress/wp-includes/ID3/
H A Dmodule.audio.ogg.php704 $readlength = self::OggPageSegmentLength($info['ogg']['pageheader'][$VorbisCommentPage], 1);
705 if ($readlength <= 0) {
709 $commentdata .= $this->fread($readlength);
/dports/chinese/wordpress-zh_TW/wordpress/wp-includes/ID3/
H A Dmodule.audio.ogg.php704 $readlength = self::OggPageSegmentLength($info['ogg']['pageheader'][$VorbisCommentPage], 1);
705 if ($readlength <= 0) {
709 $commentdata .= $this->fread($readlength);
/dports/audio/ampache/ampache-php74-5.0.0/vendor/james-heinrich/getid3/getid3/
H A Dmodule.audio.ogg.php705 $readlength = self::OggPageSegmentLength($info['ogg']['pageheader'][$VorbisCommentPage], 1);
706 if ($readlength <= 0) {
710 $commentdata .= $this->fread($readlength);
/dports/lang/spidermonkey60/firefox-60.9.0/modules/pdfium/pdfium/core/fxcodec/codec/
H A Dfx_codec_jpx_opj.cpp41 OPJ_SIZE_T readlength = nb_bytes < bufferLength ? nb_bytes : bufferLength; in opj_read_from_memory() local
42 memcpy(p_buffer, &srcData->src_data[srcData->offset], readlength); in opj_read_from_memory()
43 srcData->offset += readlength; in opj_read_from_memory()
44 return readlength; in opj_read_from_memory()
/dports/editors/texmaker/texmaker-5.0.3/pdfium/core/fxcodec/codec/
H A Dfx_codec_jpx_opj.cpp40 OPJ_SIZE_T readlength = nb_bytes < bufferLength ? nb_bytes : bufferLength; in opj_read_from_memory() local
41 memcpy(p_buffer, &srcData->src_data[srcData->offset], readlength); in opj_read_from_memory()
42 srcData->offset += readlength; in opj_read_from_memory()
43 return readlength; in opj_read_from_memory()
/dports/mail/claws-mail-perl/claws-mail-3.18.0/src/
H A Dprocmime.c664 gint restlength, readlength; in procmime_get_part_to_stream() local
687 …while ((restlength > 0) && ((readlength = claws_fread(buf, 1, restlength > BUFFSIZE ? BUFFSIZE : r… in procmime_get_part_to_stream()
688 if (claws_fwrite(buf, 1, readlength, outfp) != readlength) { in procmime_get_part_to_stream()
693 restlength -= readlength; in procmime_get_part_to_stream()
2675 gint length, readlength; in procmime_get_part_as_string() local
2707 readlength = claws_fread(data, length, 1, infp); in procmime_get_part_as_string()
2708 if (readlength <= 0) { in procmime_get_part_as_string()
/dports/mail/claws-mail-vcalendar/claws-mail-3.18.0/src/
H A Dprocmime.c664 gint restlength, readlength; in procmime_get_part_to_stream() local
687 …while ((restlength > 0) && ((readlength = claws_fread(buf, 1, restlength > BUFFSIZE ? BUFFSIZE : r… in procmime_get_part_to_stream()
688 if (claws_fwrite(buf, 1, readlength, outfp) != readlength) { in procmime_get_part_to_stream()
693 restlength -= readlength; in procmime_get_part_to_stream()
2675 gint length, readlength; in procmime_get_part_as_string() local
2707 readlength = claws_fread(data, length, 1, infp); in procmime_get_part_as_string()
2708 if (readlength <= 0) { in procmime_get_part_as_string()

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