/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/clipping/ |
H A D | ReadClipperUnitTest.java | 44 for (final Cigar cigar : cigarList) { in testHardClipBothEndsByReferenceCoordinates() 60 for (final Cigar cigar : cigarList) { in testHardClipByReferenceCoordinates() 85 for (final Cigar cigar : cigarList) { in testHardClipByReferenceCoordinatesLeftTail() 105 for (final Cigar cigar : cigarList) { in testHardClipByReferenceCoordinatesRightTail() 128 for (final Cigar cigar : cigarList) { in testHardClipLowQualEnds() 168 for (final Cigar cigar : cigarList) { in testHardClipSoftClippedBases() 181 for (final Cigar cigar : cigarList) { in testRevertSoftClippedBases() 203 for (final Cigar cigar : cigarList) { in testRevertSoftClippedBasesWithThreshold() 385 for (final Cigar cigar : cigarList) { in testSoftClipBothEndsByReferenceCoordinates() 418 for (final Cigar cigar : cigarList) { in testSoftClipByReferenceCoordinates() [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/pairwise_sequence_alignment/ |
H A D | assignment5.cpp.stdout | 2 Hit at position 0 total edits: 1 cigar: 5M 3 Hit at position 1 total edits: 1 cigar: 1I4M 4 Hit at position 2 total edits: 1 cigar: 4M1I 5 Hit at position 3 total edits: 0 cigar: 5M 6 Hit at position 4 total edits: 1 cigar: 1I4M 7 Hit at position 6 total edits: 2 cigar: 5M 8 Hit at position 14 total edits: 2 cigar: 4M1I
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H A D | assignment5_step6.cpp.stdout | 2 Hit at position 0 total edits: 1 cigar: 5M 3 Hit at position 1 total edits: 1 cigar: 1I4M 4 Hit at position 2 total edits: 1 cigar: 4M1I 5 Hit at position 3 total edits: 0 cigar: 5M 6 Hit at position 4 total edits: 1 cigar: 1I4M 7 Hit at position 6 total edits: 2 cigar: 5M 8 Hit at position 14 total edits: 2 cigar: 4M1I
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/dports/biology/samtools/samtools-1.14/misc/ |
H A D | novo2sam.pl | 222 my $cigar= ""; 240 $cigar.=$len."M"; 247 $cigar.="D"; 254 $cigar.="I"; 258 $cigar.=$len."I"; 267 $cigar.=$len."M"; 271 $cigar = newcigar($cigar,'D'); 272 $cigar = newcigar($cigar,'I'); 276 return $cigar; 283 my $cigar = shift; [all …]
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/dports/biology/seqan1/seqan-1.3.1/lib/samtools/misc/ |
H A D | novo2sam.pl | 199 my $cigar= ""; 217 $cigar.=$len."M"; 224 $cigar.="D"; 231 $cigar.="I"; 235 $cigar.=$len."I"; 244 $cigar.=$len."M"; 248 $cigar = newcigar($cigar,'D'); 249 $cigar = newcigar($cigar,'I'); 253 return $cigar; 260 my $cigar = shift; [all …]
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/dports/biology/py-hits/hits-0.1/hits/ |
H A D | sam.py | 227 cigar = cigar[::-1] 236 cigar = cigar[::-1] 239 return cigar 1019 cigar = [(BAM_CSOFT_CLIP, before_soft)] + cigar 1023 cigar = cigar + [(BAM_CSOFT_CLIP, after_soft)] 1025 cigar = collapse_soft_clip_blocks(cigar) 1033 alignment.cigar = cigar 1084 alignment.cigar = cigar 1202 merged.cigar = left_ref.cigar[:-1] + [(BAM_CDEL, deletion_length)] + right_ref.cigar[1:] 1377 cigar = alignment.cigar [all …]
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/ |
H A D | AlignmentUtils.java | 424 final Cigar cigar = r.getCigar(); in getNumAlignmentBlocks() local 425 if (cigar == null) return 0; in getNumAlignmentBlocks() 447 final Cigar cigar = r.getCigar(); in getNumAlignedBasesCountingSoftClips() local 448 if (cigar == null) return 0; in getNumAlignedBasesCountingSoftClips() 469 final Cigar cigar = r.getCigar(); in getNumHardClippedBases() local 470 if (cigar == null) return 0; in getNumHardClippedBases() 606 Utils.nonNull(cigar); in isInsideDeletion() 652 Utils.nonNull(cigar); in readToAlignmentByteArray() 942 Utils.nonNull(cigar); in startsOrEndsWithInsertionOrDeletion() 944 if ( cigar.isEmpty() ) in startsOrEndsWithInsertionOrDeletion() [all …]
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/dports/biology/stacks/stacks-2.4/src/ |
H A D | locus.cc | 154 uint size = cigar.size(); in adjust_snps_for_gaps() 163 op = cigar[i].first; in adjust_snps_for_gaps() 164 dist = cigar[i].second; in adjust_snps_for_gaps() 193 uint size = cigar.size(); in adjust_and_add_snps_for_gaps() 205 op = cigar[i].first; in adjust_and_add_snps_for_gaps() 206 dist = cigar[i].second; in adjust_and_add_snps_for_gaps() 247 uint size = cigar.size(); in remove_snps_from_gaps() 258 op = cigar[i].first; in remove_snps_from_gaps() 331 m->cigar = cigar; in add_match() 424 if (r.cigar.empty() || r.cigar.back().first != 'M' || r.cigar.back().second <= to_clip) in hard_clip_right_Ns() [all …]
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/dports/biology/py-pysam/pysam-0.18.0/samtools/ |
H A D | bam_color.c | 53 uint32_t cigar = bam_get_cigar(b)[0]; in bam_aux_getCSi() local 54 if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { in bam_aux_getCSi() 55 i -= cigar >> BAM_CIGAR_SHIFT; in bam_aux_getCSi() 82 uint32_t cigar = bam_get_cigar(b)[0]; in bam_aux_getCQi() local 83 if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { in bam_aux_getCQi() 84 i -= (cigar >> BAM_CIGAR_SHIFT); in bam_aux_getCQi() 143 uint32_t cigar = bam_get_cigar(b)[0]; in bam_aux_getCEi() local 144 if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { in bam_aux_getCEi() 145 cs_i -= cigar >> BAM_CIGAR_SHIFT; in bam_aux_getCEi()
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H A D | bam_color.c.pysam.c | 55 uint32_t cigar = bam_get_cigar(b)[0]; in bam_aux_getCSi() local 56 if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { in bam_aux_getCSi() 57 i -= cigar >> BAM_CIGAR_SHIFT; in bam_aux_getCSi() 84 uint32_t cigar = bam_get_cigar(b)[0]; in bam_aux_getCQi() local 85 if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { in bam_aux_getCQi() 86 i -= (cigar >> BAM_CIGAR_SHIFT); in bam_aux_getCQi() 145 uint32_t cigar = bam_get_cigar(b)[0]; in bam_aux_getCEi() local 146 if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { in bam_aux_getCEi() 147 cs_i -= cigar >> BAM_CIGAR_SHIFT; in bam_aux_getCEi()
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/dports/biology/samtools/samtools-1.14/ |
H A D | bam_color.c | 53 uint32_t cigar = bam_get_cigar(b)[0]; in bam_aux_getCSi() local 54 if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { in bam_aux_getCSi() 55 i -= cigar >> BAM_CIGAR_SHIFT; in bam_aux_getCSi() 82 uint32_t cigar = bam_get_cigar(b)[0]; in bam_aux_getCQi() local 83 if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { in bam_aux_getCQi() 84 i -= (cigar >> BAM_CIGAR_SHIFT); in bam_aux_getCQi() 143 uint32_t cigar = bam_get_cigar(b)[0]; in bam_aux_getCEi() local 144 if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { in bam_aux_getCEi() 145 cs_i -= cigar >> BAM_CIGAR_SHIFT; in bam_aux_getCEi()
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/dports/biology/vcflib/vcflib-1.0.2/src/ |
H A D | ssw_cpp.cpp | 70 al->cigar.clear(); in ConvertAlignment() 77 al->cigar.push_back(cigar); in ConvertAlignment() 82 al->cigar.push_back(s_al.cigar[i]); in ConvertAlignment() 83 cigar_string << cigar_int_to_len(s_al.cigar[i]) << cigar_int_to_op(s_al.cigar[i]); in ConvertAlignment() 89 al->cigar.push_back(cigar); in ConvertAlignment() 147 new_cigar.push_back(cigar); in CalculateNumberMismatch() 190 new_cigar.push_back(al->cigar[i]); in CalculateNumberMismatch() 196 new_cigar.push_back(al->cigar[i]); in CalculateNumberMismatch() 206 new_cigar.push_back(cigar); in CalculateNumberMismatch() 211 al->cigar.clear(); in CalculateNumberMismatch() [all …]
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/dports/biology/freebayes/freebayes-1.3.5/vcflib-temp/src/ |
H A D | ssw_cpp.cpp | 61 al->cigar.clear(); in ConvertAlignment() 68 al->cigar.push_back(cigar); in ConvertAlignment() 73 al->cigar.push_back(s_al.cigar[i]); in ConvertAlignment() 74 cigar_string << cigar_int_to_len(s_al.cigar[i]) << cigar_int_to_op(s_al.cigar[i]); in ConvertAlignment() 80 al->cigar.push_back(cigar); in ConvertAlignment() 138 new_cigar.push_back(cigar); in CalculateNumberMismatch() 181 new_cigar.push_back(al->cigar[i]); in CalculateNumberMismatch() 187 new_cigar.push_back(al->cigar[i]); in CalculateNumberMismatch() 197 new_cigar.push_back(cigar); in CalculateNumberMismatch() 202 al->cigar.clear(); in CalculateNumberMismatch() [all …]
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/dports/biology/freebayes/freebayes-1.3.5/contrib/SeqLib/src/ |
H A D | ssw_cpp.cpp | 61 al->cigar.clear(); in ConvertAlignment() 68 al->cigar.push_back(cigar); in ConvertAlignment() 73 al->cigar.push_back(s_al.cigar[i]); in ConvertAlignment() 74 cigar_string << cigar_int_to_len(s_al.cigar[i]) << cigar_int_to_op(s_al.cigar[i]); in ConvertAlignment() 80 al->cigar.push_back(cigar); in ConvertAlignment() 138 new_cigar.push_back(cigar); in CalculateNumberMismatch() 181 new_cigar.push_back(al->cigar[i]); in CalculateNumberMismatch() 187 new_cigar.push_back(al->cigar[i]); in CalculateNumberMismatch() 197 new_cigar.push_back(cigar); in CalculateNumberMismatch() 202 al->cigar.clear(); in CalculateNumberMismatch() [all …]
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/dports/biology/freebayes/freebayes-1.3.5/vcflib/src/ |
H A D | ssw_cpp.cpp | 61 al->cigar.clear(); in ConvertAlignment() 68 al->cigar.push_back(cigar); in ConvertAlignment() 73 al->cigar.push_back(s_al.cigar[i]); in ConvertAlignment() 74 cigar_string << cigar_int_to_len(s_al.cigar[i]) << cigar_int_to_op(s_al.cigar[i]); in ConvertAlignment() 80 al->cigar.push_back(cigar); in ConvertAlignment() 138 new_cigar.push_back(cigar); in CalculateNumberMismatch() 181 new_cigar.push_back(al->cigar[i]); in CalculateNumberMismatch() 187 new_cigar.push_back(al->cigar[i]); in CalculateNumberMismatch() 197 new_cigar.push_back(cigar); in CalculateNumberMismatch() 202 al->cigar.clear(); in CalculateNumberMismatch() [all …]
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/dports/biology/bowtie2/bowtie2-2.4.4/scripts/sim/ |
H A D | AlignmentCheck.pm | 313 my ($cigar, $ops, $runs) = @_; 315 while($i < length($cigar)) { 319 $i < length($cigar) || die; 332 my ($seq, $cigar) = @_; 355 my ($cigar) = @_; 359 while($i < length($cigar)) { 364 $i < length($cigar) || die; 428 my ($seq, $md, $cigar) = @_; 515 my $cigar = $1; 516 defined($cigar) || [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/gustaf/example/ |
H A D | stellar_joinedMates.gff | 1 …atches 4546 4690 96.5986 + . deletion;seq2Range=75,220;eValue=1.96977e-63;cigar=1M1D1M1I2M1I140M;m… 2 …Stellar eps-matches 1 97 100 + . deletion;seq2Range=124,220;eValue=2.41424e-45;cigar=97M;mutations= 3 …-matches 3532 3578 95.8333 + . deletion;seq2Range=1,47;eValue=6.41732e-17;cigar=41M1I2M1D3M;mutati… 4 …matches 3706 3751 95.6521 + . deletion;seq2Range=36,80;eValue=6.93385e-16;cigar=3M1D42M;mutations=… 5 …atches 3501 3581 95.1219 + . deletion_2;seq2Range=1,79;eValue=1.33056e-31;cigar=72M1I2M1D3M2D1M;mu… 6 …ches 3700 3780 95.1219 + . deletion_2;seq2Range=61,140;eValue=1.33056e-31;cigar=2M1D4M1I2M1D71M;mu… 7 …-matches 75 143 95.6521 - . deletion;seq2Range=106,174;eValue=3.19717e-26;cigar=69M;mutations=61T,… 8 …tches 4671 4718 95.8333 - . deletion;seq2Range=124,171;eValue=6.41732e-17;cigar=48M;mutations=43T,…
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H A D | stellar_joinedMates_l30.gff | 1 …atches 4546 4690 96.5986 + . deletion;seq2Range=75,220;eValue=1.96977e-63;cigar=1M1D1M1I2M1I140M;m… 2 …Stellar eps-matches 1 97 100 + . deletion;seq2Range=124,220;eValue=2.41424e-45;cigar=97M;mutations= 3 …-matches 3532 3578 95.8333 + . deletion;seq2Range=1,47;eValue=6.41732e-17;cigar=41M1I2M1D3M;mutati… 4 …matches 3706 3751 95.6521 + . deletion;seq2Range=36,80;eValue=6.93385e-16;cigar=3M1D42M;mutations=… 5 …atches 3501 3581 95.1219 + . deletion_2;seq2Range=1,79;eValue=1.33056e-31;cigar=72M1I2M1D3M2D1M;mu… 6 …ches 3700 3780 95.1219 + . deletion_2;seq2Range=61,140;eValue=1.33056e-31;cigar=2M1D4M1I2M1D71M;mu… 7 …-matches 75 143 95.6521 - . deletion;seq2Range=106,174;eValue=3.19717e-26;cigar=69M;mutations=61T,… 8 …tches 4671 4718 95.8333 - . deletion;seq2Range=124,171;eValue=6.41732e-17;cigar=48M;mutations=43T,…
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/dports/biology/hisat2/hisat2-2.2.1/scripts/sim/ |
H A D | AlignmentCheck.pm | 313 my ($cigar, $ops, $runs) = @_; 315 while($i < length($cigar)) { 319 $i < length($cigar) || die; 332 my ($seq, $cigar) = @_; 355 my ($cigar) = @_; 359 while($i < length($cigar)) { 364 $i < length($cigar) || die; 428 my ($seq, $md, $cigar) = @_; 515 my $cigar = $1; 516 defined($cigar) || [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers/tests/ |
H A D | se-adeno-reads36_1-id-of3.gff | 3 ….1| razers read 9 44 97.2222 - . ID=adeno-reads36.fasta.000000852;suboptimal;cigar=36M;mutations=2C 4 …7.1| razers read 25 59 97.2222 - . ID=adeno-reads36.fasta.000000024;multi;cigar=15M1I20M;mutations… 31 ….1| razers read 201 236 97.2222 + . ID=adeno-reads36.fasta.000000197;unique;cigar=36M;mutations=26T 57 …NC_002077.1| razers read 336 372 97.2222 + . ID=adeno-reads36.fasta.000000804;unique;cigar=10M1D26M 107 …NC_002077.1| razers read 511 547 97.2222 + . ID=adeno-reads36.fasta.000000169;unique;cigar=15M1D21M 141 …NC_002077.1| razers read 659 695 97.2222 + . ID=adeno-reads36.fasta.000000443;unique;cigar=25M1D11M 266 …C_002077.1| razers read 1272 1308 97.2222 + . ID=adeno-reads36.fasta.000000010;unique;cigar=32M1D4M 305 …_002077.1| razers read 1449 1485 97.2222 - . ID=adeno-reads36.fasta.000000636;unique;cigar=15M1D21M 347 …C_002077.1| razers read 1661 1697 97.2222 - . ID=adeno-reads36.fasta.000000474;unique;cigar=6M1D30M 537 …C_002077.1| razers read 2463 2499 97.2222 - . ID=adeno-reads36.fasta.000000200;unique;cigar=32M1D4M [all …]
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H A D | pe-adeno-reads100_2-id-of3.gff | 4 …7.1| razers read 301 400 99 + . ID=adeno-reads100.fasta.000000592/L;unique;cigar=100M;mutations=77A 5 …7.1| razers read 304 403 99 - . ID=adeno-reads100.fasta.000000686/L;unique;cigar=100M;mutations=67A 10 …77.1| razers read 570 669 99 + . ID=adeno-reads100.fasta.000000670/L;multi;cigar=100M;mutations=66C 11 …77.1| razers read 570 669 99 + . ID=adeno-reads100.fasta.000000670/L;multi;cigar=100M;mutations=66C 17 ….1| razers read 689 789 98 + . ID=adeno-reads100.fasta.000000388/L;unique;cigar=97M1D3M;mutations=… 77 …f|NC_002077.1| razers read 1880 1980 99 - . ID=adeno-reads100.fasta.000000360/L;multi;cigar=98M1D2M 78 …f|NC_002077.1| razers read 1880 1980 99 - . ID=adeno-reads100.fasta.000000360/L;multi;cigar=98M1D2M 80 …7.1| razers read 1909 2008 99 + . ID=adeno-reads100.fasta.000000139/L;multi;cigar=100M;mutations=2A 81 …7.1| razers read 1909 2008 99 + . ID=adeno-reads100.fasta.000000139/L;multi;cigar=100M;mutations=2A 84 …|NC_002077.1| razers read 2010 2110 99 - . ID=adeno-reads100.fasta.000000863/L;unique;cigar=6M1D94M [all …]
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/bam_io/ |
H A D | bam_alignment_record_util.h | 109 for (unsigned j = 0; j < length(record.cigar); ++j) in getClippedPos() 111 if (record.cigar[j].operation == 'S') in getClippedPos() 112 posBegin += record.cigar[j].count; in getClippedPos() 116 for (unsigned j = 0; j < length(record.cigar); ++j) in getClippedPos() 118 if (record.cigar[length(record.cigar) - j - 1].operation == 'S') in getClippedPos() 119 posEnd -= record.cigar[length(record.cigar) - j - 1].count; in getClippedPos() 240 unsigned len = getAlignmentLengthInRef(record) - countPaddings(record.cigar); in bamRecordToAlignment() 245 cigarToGapAnchorContig(row(result, 0), record.cigar); in bamRecordToAlignment() 248 cigarToGapAnchorRead(row(result, 1), record.cigar); in bamRecordToAlignment()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/bam_io/ |
H A D | bam_alignment_record_util.h | 109 for (unsigned j = 0; j < length(record.cigar); ++j) in getClippedPos() 111 if (record.cigar[j].operation == 'S') in getClippedPos() 112 posBegin += record.cigar[j].count; in getClippedPos() 116 for (unsigned j = 0; j < length(record.cigar); ++j) in getClippedPos() 118 if (record.cigar[length(record.cigar) - j - 1].operation == 'S') in getClippedPos() 119 posEnd -= record.cigar[length(record.cigar) - j - 1].count; in getClippedPos() 240 unsigned len = getAlignmentLengthInRef(record) - countPaddings(record.cigar); in bamRecordToAlignment() 245 cigarToGapAnchorContig(row(result, 0), record.cigar); in bamRecordToAlignment() 248 cigarToGapAnchorRead(row(result, 1), record.cigar); in bamRecordToAlignment()
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/bam_io/ |
H A D | bam_alignment_record_util.h | 109 for (unsigned j = 0; j < length(record.cigar); ++j) in getClippedPos() 111 if (record.cigar[j].operation == 'S') in getClippedPos() 112 posBegin += record.cigar[j].count; in getClippedPos() 116 for (unsigned j = 0; j < length(record.cigar); ++j) in getClippedPos() 118 if (record.cigar[length(record.cigar) - j - 1].operation == 'S') in getClippedPos() 119 posEnd -= record.cigar[length(record.cigar) - j - 1].count; in getClippedPos() 240 unsigned len = record.beginPos + getAlignmentLengthInRef(record) - countPaddings(record.cigar); in bamRecordToAlignment() 245 cigarToGapAnchorContig(row(result, 0), record.cigar); in bamRecordToAlignment() 248 cigarToGapAnchorRead(row(result, 1), record.cigar); in bamRecordToAlignment()
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/dports/biology/bbmap/bbmap/current/stream/ |
H A D | SamLine.java | 80 cigar=sl.cigar; in setFrom() 442 cigar=s[5]; in SamLine() 1203 assert(cigar!=null); in calcIdentity() 1270 if(cigar==null || cigar.equals(stringstar)){return null;} in toShortMatch() 1596 if(r.mapped() && cigar!=null && cigar.indexOf('N')>=0){ in makeXSTag() 1802 if(cigar==null || cigar.indexOf('N')<0){ in makeOptionalTags() 1809 if(cigar==null || cigar.indexOf('N')<0){ in makeOptionalTags() 2187 len+=(cigar==null ? 1 : cigar.length()); in textLength() 2464 if(!mapped() || cigar==null || cigar.charAt(0)=='*'){ in stop() 2575 sum+=(cigar==null ? 0 : cigar.length()*2+16); [all …]
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