| /dports/biology/freebayes/freebayes-1.3.5/test/regression/ |
| H A D | NA12878.chr22.tiny.vcf | 39 …CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele…
63 q 910 . A C 1.9784e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=3.73412;EP…
64 q 930 . T C 1.78554e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=34;DPB=34;DPRA=0;EPP=9.52472;E…
68 q 952 . T C 0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=7.35324;EPPR=3.9754…
79 q 1781 . C A 0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=7.35324;EPPR=8.684…
85 q 2201 . C A 0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=7.35324;EPPR=5.886…
131 q 4129 . A G 0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=7.35324;EPPR=6.870…
133 q 4144 . C A 0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=3.0103;EPPR=4.6553…
162 q 7152 . C A 0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=3.0103;EPPR=3.9754…
163 q 7159 . C A 0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=7.35324;EPPR=8.724…
[all …]
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| /dports/biology/bamutil/bamUtil-1.0.15/test/testFiles/ |
| H A D | README | 9 All fields are valid. CIGAR is "*" & MRNM is "=". No Tags.
13 All fields are valid. CIGAR, SEQ, & QUAL are "*". Tags are used.
21 …All fields are valid. RNAME, CIGAR, MRNMAN are "=". POS, MAPQ, MPOS, and ISIZE are "0". No Tags.
25 …All fields are valid. RNAME, CIGAR, MRNMAN are "=". POS, MAPQ, MPOS, and ISIZE are "0". SEQ & Q…
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| /dports/biology/sra-tools/sra-tools-2.11.0/tools2/assemble-fragments/ |
| H A D | fragment.hpp | 193 struct CIGAR : public std::vector<CIGAR_OP> { struct
200 …CIGAR(unsigned rlength, unsigned left_clip, unsigned qlength, unsigned right_clip, std::vector<CIG… in CIGAR() argument
208 CIGAR() in CIGAR() argument
214 explicit CIGAR(std::string const &str) in CIGAR() argument
314 CIGAR adjoint() const { in adjoint() argument
315 return CIGAR(rlength, qclip, qlength, qfirst, std::vector<CIGAR_OP>(rbegin(), rend())); in adjoint()
323 CIGAR cigar;
337 …const &sequence, std::string const &reference, char strand, int position, std::string const &CIGAR) in Alignment()
344 , cigarString(CIGAR) in Alignment()
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| H A D | sam2ir.cpp | 52 auto const &CIGAR = fields[5]; in writeRow() local
54 …auto const isAligned = (flags & 0x04) == 0 ? ((position > 0) && RNAME != "*" && CIGAR != "*") : fa… in writeRow()
68 out.value(8, CIGAR); in writeRow()
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| /dports/biology/sra-tools/sra-tools-2.11.0/tools/bam-loader/ |
| H A D | SAM-fuzzer.pl | 182 CIGAR => '*',
245 $rec->{CIGAR} = "0H0S0M0I0D0N0=0X0S0H";
250 $rec->{CIGAR} = 0xFFFFFFF . 'M';
478 $_[0]->{CIGAR},
715 … $_[0]->{FLAG} |= 0x0004 if ($_[0]->{CIGAR} eq '*' || $_[0]->{RNAME} eq '*' || $_[0]->{POS} == 0);
722 $_[0]->{CIGAR} = '*';
758 $result->{CIGAR} = random_CIGAR($seqlen);
761 $result->{CIGAR} = random_CIGAR(int(rand(0xFFFFFF0) + 0x0F));
788 $_[0]->{CIGAR} = random_CIGAR($seqlen);
789 $_[1]->{CIGAR} = random_CIGAR($seqlen);
[all …]
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| /dports/biology/star/STAR-2.7.9a/source/ |
| H A D | Transcript_generateCigarP.cpp | 8 string CIGAR; in generateCigarP() local
60 CIGAR=samStreamCIGAR.str(); in generateCigarP()
62 return CIGAR; in generateCigarP()
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| H A D | ReadAlign_outputTranscriptCIGARp.cpp | 7 string CIGAR; in outputTranscriptCIGARp() local
59 CIGAR=samStreamCIGAR.str(); in outputTranscriptCIGARp()
61 return CIGAR; in outputTranscriptCIGARp()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/readers/bam/test/ |
| H A D | bam_compare.cpp | 137 string CIGAR = it.GetCIGAR(); in GetShortSeqData() local
138 const char* ptr = CIGAR.data(); in GetShortSeqData()
139 const char* end = ptr + CIGAR.size(); in GetShortSeqData()
413 it.GetRawCIGAR(aln.CIGAR); in Run()
497 it.GetRawCIGAR(aln.CIGAR); in Run()
832 if ( !a.CIGAR.empty() && (a.CIGAR.back() & 0xf) == 5 ) { in Run()
833 a.CIGAR.pop_back(); in Run()
835 if ( !a.CIGAR.empty() && (a.CIGAR.front() & 0xf) == 5 ) { in Run()
836 a.CIGAR.erase(a.CIGAR.begin()); in Run()
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| H A D | samtools.cpp | 49 ORDER_BY(CIGAR);
65 ORDER_BY(CIGAR); in operator ==()
80 ITERATE ( vector<Uint4>, i, a.CIGAR ) { in operator <<()
146 aln.CIGAR.assign(cigar, cigar+cigar_len); in bam_collect_func()
148 ITERATE ( vector<Uint4>, i, aln.CIGAR ) { in bam_collect_func()
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| /dports/biology/freebayes/freebayes-1.3.5/src/ |
| H A D | LeftAlign.cpp | 43 CIGAR cigar = alignment.GETCIGAR; in leftAlign()
44 for (CIGAR::const_iterator c = cigar.begin(); in leftAlign()
246 CIGAR newCigar; in leftAlign()
309 CIGAR cigar = alignment.GETCIGAR; in leftAlign()
310 for (CIGAR::const_iterator c = cigar.begin(); in leftAlign()
327 for (CIGAR::const_iterator c = cigar.begin(); in leftAlign()
350 CIGAR cigar = alignment.GETCIGAR; in countMismatches()
351 for (CIGAR::const_iterator c = cigar.begin(); in countMismatches()
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| H A D | LeftAlign.h | 43 #define CIGAR std::vector<CigarOp> macro
85 #define CIGAR SeqLib::Cigar macro
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| /dports/biology/sra-tools/sra-tools-2.11.0/test/samline/ |
| H A D | sec_align_problem.sh | 21 CIGAR="-c 55M"
26 …execute "$SAMLINE_BINARY $QNAME $REFNAME $REFPOS $CIGAR $SECONDARY $FIRST $WITH_HEADERS $CREATE_CO…
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| /dports/biology/bio-mocha/bcftools-1.14/test/ |
| H A D | view.vectors.A.out | 17 ##INFO=<ID=CIGAR,Number=A,Type=String,Description="test">
53 1 3162007 . TAGGG CAGGG 238 PASS AO=52101;CIGAR=1X4M;AC=1;AN=2 GT:FGS:FGI:FGF:FAS:FAI:FAF:FRS:FRI:F…
54 1 3162008 . TAGGG CAGGG 238 PASS IA8=10,.;IA16=1000,.;IA32=100000,.;IAF=0.003,.;CIGAR=1X4M;AC=1;AN=…
55 1 3162009 . TAGGG CAGGG 238 PASS IA8=.;IA16=.;IA32=.;IAF=.;CIGAR=1X4M;AC=1;AN=2 GT:F8:F16:F32:FF 0/…
56 1 3162010 . TAGGG CAGGG 238 PASS I8=.;I16=.;I32=.;IF=.;CIGAR=1X4M;AC=1;AN=2 GT:F8:F16:F32:FF 0/1:10…
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| H A D | view.vectors.B.out | 17 ##INFO=<ID=CIGAR,Number=A,Type=String,Description="test">
53 1 3162007 . TAGGG CAGGT 238 PASS AO=113;CIGAR=1X3M1X;AC=1;AN=1 GT:FGS:FGI:FGF:FAS:FAI:FAF:FRS:FRI:F…
54 1 3162008 . TAGGG CAGGT 238 PASS IA8=10,.;IA16=1000,.;IA32=100000,.;IAF=0.003,.;CIGAR=1X3M1X;AC=1;A…
55 1 3162009 . TAGGG CAGGT 238 PASS IA8=.;IA16=.;IA32=.;IAF=.;CIGAR=1X3M1X;AC=1;AN=1 GT:F8:F16:F32:FF …
56 1 3162010 . TAGGG CAGGT 238 PASS I8=.;I16=.;I32=.;IF=.;CIGAR=1X3M1X;AC=1;AN=1 GT:F8:F16:F32:FF 1:.:…
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| H A D | view.vectors.vcf | 16 ##INFO=<ID=CIGAR,Number=A,Type=String,Description="test">
52 1 3162007 . TAGGG CAGGG,CAGGT 238 PASS AO=52101,113;CIGAR=1X4M,1X3M1X GT:FGS:FGI:FGF:FAS:FAI:FAF:FR…
53 1 3162008 . TAGGG CAGGG,CAGGT 238 PASS IA8=10,.;IA16=1000,.;IA32=100000,.;IAF=3e-3,.;CIGAR=1X4M,1X3…
54 1 3162009 . TAGGG CAGGG,CAGGT 238 PASS IA8=.;IA16=.;IA32=.;IAF=.;CIGAR=1X4M,1X3M1X GT:F8:F16:F32:FF…
55 1 3162010 . TAGGG CAGGG,CAGGT 238 PASS I8=.;I16=.;I32=.;IF=.;CIGAR=1X4M,1X3M1X GT:F8:F16:F32:FF 0/1…
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| /dports/biology/bcftools/bcftools-1.14/test/ |
| H A D | view.vectors.B.out | 17 ##INFO=<ID=CIGAR,Number=A,Type=String,Description="test">
53 1 3162007 . TAGGG CAGGT 238 PASS AO=113;CIGAR=1X3M1X;AC=1;AN=1 GT:FGS:FGI:FGF:FAS:FAI:FAF:FRS:FRI:F…
54 1 3162008 . TAGGG CAGGT 238 PASS IA8=10,.;IA16=1000,.;IA32=100000,.;IAF=0.003,.;CIGAR=1X3M1X;AC=1;A…
55 1 3162009 . TAGGG CAGGT 238 PASS IA8=.;IA16=.;IA32=.;IAF=.;CIGAR=1X3M1X;AC=1;AN=1 GT:F8:F16:F32:FF …
56 1 3162010 . TAGGG CAGGT 238 PASS I8=.;I16=.;I32=.;IF=.;CIGAR=1X3M1X;AC=1;AN=1 GT:F8:F16:F32:FF 1:.:…
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| H A D | view.vectors.A.out | 17 ##INFO=<ID=CIGAR,Number=A,Type=String,Description="test">
53 1 3162007 . TAGGG CAGGG 238 PASS AO=52101;CIGAR=1X4M;AC=1;AN=2 GT:FGS:FGI:FGF:FAS:FAI:FAF:FRS:FRI:F…
54 1 3162008 . TAGGG CAGGG 238 PASS IA8=10,.;IA16=1000,.;IA32=100000,.;IAF=0.003,.;CIGAR=1X4M;AC=1;AN=…
55 1 3162009 . TAGGG CAGGG 238 PASS IA8=.;IA16=.;IA32=.;IAF=.;CIGAR=1X4M;AC=1;AN=2 GT:F8:F16:F32:FF 0/…
56 1 3162010 . TAGGG CAGGG 238 PASS I8=.;I16=.;I32=.;IF=.;CIGAR=1X4M;AC=1;AN=2 GT:F8:F16:F32:FF 0/1:10…
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| H A D | view.vectors.vcf | 16 ##INFO=<ID=CIGAR,Number=A,Type=String,Description="test">
52 1 3162007 . TAGGG CAGGG,CAGGT 238 PASS AO=52101,113;CIGAR=1X4M,1X3M1X GT:FGS:FGI:FGF:FAS:FAI:FAF:FR…
53 1 3162008 . TAGGG CAGGG,CAGGT 238 PASS IA8=10,.;IA16=1000,.;IA32=100000,.;IAF=3e-3,.;CIGAR=1X4M,1X3…
54 1 3162009 . TAGGG CAGGG,CAGGT 238 PASS IA8=.;IA16=.;IA32=.;IAF=.;CIGAR=1X4M,1X3M1X GT:F8:F16:F32:FF…
55 1 3162010 . TAGGG CAGGG,CAGGT 238 PASS I8=.;I16=.;I32=.;IF=.;CIGAR=1X4M,1X3M1X GT:F8:F16:F32:FF 0/1…
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| /dports/biology/bedtools/bedtools2-2.30.0/docs/content/tools/ |
| H A D | bamtobed.rst | 42 "spliced" BAM alignments (denoted by the "N" CIGAR operation)
44 **-split** Report each portion of a "split" BAM (i.e., having an "N" CIGAR
46 **-splitD** Report each portion of a "split" BAM while obeying both "N" CIGAR
57 **-cigar** Add the CIGAR string to the BED entry as a 7th column.
110 their respective CIGAR strings. It also assumes that the
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| H A D | bedtobam.rst | 23 …res (e.g., gene annotations) into "spliced" BAM alignments by creating an appropriate CIGAR string.
57 -bed12 option. This will create CIGAR strings in the BAM output that will be displayed as "spliced"
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| /dports/biology/sam2pairwise/sam2pairwise-1.0.0/ |
| H A D | README.md | 4 sam2pairwise takes a SAM file and uses the CIGAR and MD tag to reconstruct the pairwise alignment o…
45 sam2pairwise currently supports the following CIGAR elements for reconstructing the alignment:
70 …ot detected & the CIGAR contains characters that require the MD tag to resolve, or if an unsupport…
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| /dports/biology/emboss/EMBOSS-6.6.0/ajax/core/ |
| H A D | ajassemwrite.c | 1384 AjPStr CIGAR = NULL; in assemoutWriteSamAlignment() local
1466 ajDebug("cigar: %S\n", CIGAR); in assemoutWriteSamAlignment()
1468 ajStrAssignS(&tmp, CIGAR); in assemoutWriteSamAlignment()
1473 ajFmtPrintS(&CIGAR, "%dS%S", in assemoutWriteSamAlignment()
1476 ajFmtPrintAppS(&CIGAR, "%dS", r->x2 - 1); in assemoutWriteSamAlignment()
1481 ajFmtPrintS(&CIGAR, "%dS%S", r->x2 - 1, tmp); in assemoutWriteSamAlignment()
1483 ajFmtPrintAppS(&CIGAR, "%dS", in assemoutWriteSamAlignment()
1492 ajStrAssignK(&CIGAR, '*'); in assemoutWriteSamAlignment()
1495 ajStrAssignK(&CIGAR, '*'); in assemoutWriteSamAlignment()
1513 (CIGAR ? CIGAR : r->Cigar), in assemoutWriteSamAlignment()
[all …]
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| /dports/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/ |
| H A D | CigarOperation.inl | 18 …throw std::runtime_error{"CIGAR operation 'M' is not allowed in PacBio BAM files. Use 'X/=' instea…
28 …throw std::runtime_error{"CIGAR operation 'M' is not allowed in PacBio BAM files. Use 'X/=' instea…
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| /dports/biology/sra-tools/sra-tools-2.11.0/tools2/shared/schema/ |
| H A D | aligned-ir.schema.text | 43 extern column <ascii> zip_encoding CIGAR;
121 …extern column <ascii> zip_encoding CIGAR; ///< the CIGAR, as given, of the 5'-most mate + "0P" + …
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/htsgetreader/ |
| H A D | HtsgetRequestField.java | 12 CIGAR, enumConstant
|