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Searched refs:cigar (Results 126 – 150 of 1306) sorted by relevance

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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/clipping/
H A DReadClipperUnitTest.java44 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 …]
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/pairwise_sequence_alignment/
H A Dassignment5.cpp.stdout2 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
H A Dassignment5_step6.cpp.stdout2 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
/dports/biology/samtools/samtools-1.14/misc/
H A Dnovo2sam.pl222 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 …]
/dports/biology/seqan1/seqan-1.3.1/lib/samtools/misc/
H A Dnovo2sam.pl199 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 …]
/dports/biology/py-hits/hits-0.1/hits/
H A Dsam.py227 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 …]
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/
H A DAlignmentUtils.java424 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 …]
/dports/biology/stacks/stacks-2.4/src/
H A Dlocus.cc154 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 …]
/dports/biology/py-pysam/pysam-0.18.0/samtools/
H A Dbam_color.c53 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()
H A Dbam_color.c.pysam.c55 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()
/dports/biology/samtools/samtools-1.14/
H A Dbam_color.c53 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()
/dports/biology/vcflib/vcflib-1.0.2/src/
H A Dssw_cpp.cpp70 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 …]
/dports/biology/freebayes/freebayes-1.3.5/vcflib-temp/src/
H A Dssw_cpp.cpp61 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 …]
/dports/biology/freebayes/freebayes-1.3.5/contrib/SeqLib/src/
H A Dssw_cpp.cpp61 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 …]
/dports/biology/freebayes/freebayes-1.3.5/vcflib/src/
H A Dssw_cpp.cpp61 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 …]
/dports/biology/bowtie2/bowtie2-2.4.4/scripts/sim/
H A DAlignmentCheck.pm313 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 …]
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/gustaf/example/
H A Dstellar_joinedMates.gff1 …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,…
H A Dstellar_joinedMates_l30.gff1 …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,…
/dports/biology/hisat2/hisat2-2.2.1/scripts/sim/
H A DAlignmentCheck.pm313 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 …]
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers/tests/
H A Dse-adeno-reads36_1-id-of3.gff3 ….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 …]
H A Dpe-adeno-reads100_2-id-of3.gff4 …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 …]
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/bam_io/
H A Dbam_alignment_record_util.h109 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()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/bam_io/
H A Dbam_alignment_record_util.h109 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()
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/bam_io/
H A Dbam_alignment_record_util.h109 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()
/dports/biology/bbmap/bbmap/current/stream/
H A DSamLine.java80 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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