/dports/biology/gmap/gmap-2020-09-12/src/ |
H A D | samread.c | 38 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 …]
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H A D | sam_sort.c | 855 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 …]
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H A D | samread.h | 28 Samread_parse_read_fromfile (FILE *fp, unsigned int *flag, int *readlength, char **read, int linele…
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/ |
H A D | JunctionTreeKBestHaplotypeFinderUnitTest.java | 79 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 …]
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/dports/biology/velvet/velvet_1.2.10/contrib/afg_handling/ |
H A D | snp_view.pl | 48 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)){
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/dports/net-p2p/btcheck/btcheck-2.1/src/ |
H A D | check.c | 35 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()
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/dports/comms/owfs/owfs-3.2p4/module/owlib/src/include/ |
H A D | ow_transaction.h | 134 #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) )
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/dports/www/chromium-legacy/chromium-88.0.4324.182/third_party/pdfium/core/fxcodec/jpx/ |
H A D | jpx_decode_utils.cpp | 28 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()
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/dports/www/qt5-webengine/qtwebengine-everywhere-src-5.15.2/src/3rdparty/chromium/third_party/pdfium/core/fxcodec/jpx/ |
H A D | jpx_decode_utils.cpp | 28 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()
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/dports/devel/py-defusedxml/defusedxml-0.6.0/defusedxml/ |
H A D | xmlrpc.py | 83 self.readlength = None 86 self.readlength = 0 94 left = self.limit - self.readlength 97 self.readlength += len(data) 98 if self.readlength > self.limit:
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/pileup/ |
H A D | ReadPileupUnitTest.java | 311 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 [all …]
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/dports/science/nwchem-data/nwchem-7.0.2-release/src/lucia/ |
H A D | cio.c | 153 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;}
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/dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/lucia/ |
H A D | cio.c | 153 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;}
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/dports/net/pear-File_Bittorrent2/File_Bittorrent2-1.3.1/File/Bittorrent2/ |
H A D | MakeTorrent.php | 335 $readlength = 8192; 337 $readlength = $this->piece_length - $datalength; 340 $tmpdata = fread($this->fp, $readlength);
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/dports/graphics/exifprobe/exifprobe-2.0.1/ |
H A D | print.c | 2375 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 …]
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/dports/biology/bbmap/bbmap/current/jgi/ |
H A D | SynthMDA.java | 97 readlength=Integer.parseInt(b); in SynthMDA() 262 list.add("length="+readlength); in process() 394 private int readlength=150; field in SynthMDA
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/dports/security/shibboleth-sp/shibboleth-sp-3.3.0/shibsp/remoting/impl/ |
H A D | SocketListener.cpp | 528 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()
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/dports/www/ilias/ILIAS-5.4.25/libs/composer/vendor/james-heinrich/getid3/getid3/ |
H A D | module.audio.ogg.php | 649 $readlength = self::OggPageSegmentLength($info['ogg']['pageheader'][$VorbisCommentPage], 1); 650 if ($readlength <= 0) { 654 $commentdata .= $this->fread($readlength);
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/dports/chinese/wordpress-zh_CN/wordpress/wp-includes/ID3/ |
H A D | module.audio.ogg.php | 704 $readlength = self::OggPageSegmentLength($info['ogg']['pageheader'][$VorbisCommentPage], 1); 705 if ($readlength <= 0) { 709 $commentdata .= $this->fread($readlength);
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/dports/chinese/wordpress-zh_TW/wordpress/wp-includes/ID3/ |
H A D | module.audio.ogg.php | 704 $readlength = self::OggPageSegmentLength($info['ogg']['pageheader'][$VorbisCommentPage], 1); 705 if ($readlength <= 0) { 709 $commentdata .= $this->fread($readlength);
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/dports/audio/ampache/ampache-php74-5.0.0/vendor/james-heinrich/getid3/getid3/ |
H A D | module.audio.ogg.php | 705 $readlength = self::OggPageSegmentLength($info['ogg']['pageheader'][$VorbisCommentPage], 1); 706 if ($readlength <= 0) { 710 $commentdata .= $this->fread($readlength);
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/dports/lang/spidermonkey60/firefox-60.9.0/modules/pdfium/pdfium/core/fxcodec/codec/ |
H A D | fx_codec_jpx_opj.cpp | 41 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()
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/dports/editors/texmaker/texmaker-5.0.3/pdfium/core/fxcodec/codec/ |
H A D | fx_codec_jpx_opj.cpp | 40 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()
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/dports/mail/claws-mail-perl/claws-mail-3.18.0/src/ |
H A D | procmime.c | 664 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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/dports/mail/claws-mail-vcalendar/claws-mail-3.18.0/src/ |
H A D | procmime.c | 664 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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