| /dports/biology/freebayes/freebayes-1.3.5/contrib/SeqLib/SeqLib/ |
| H A D | BamRecord.h | 513 out += bam_cigar_oplen(c[i]); in NumAlignedBases()
524 imax = std::max(bam_cigar_oplen(c[i]), imax); in MaxInsertionBases()
534 dmax = std::max(bam_cigar_oplen(c[i]), dmax); in MaxDeletionBases()
544 dmax += bam_cigar_oplen(c[i]); in NumMatchBases()
613 p += bam_cigar_oplen(c[i]); in AlignmentPositionReverse()
628 p += bam_cigar_oplen(c[i]); in AlignmentEndPositionReverse()
643 p += bam_cigar_oplen(c[i]); in AlignmentPosition()
657 p += bam_cigar_oplen(c[i]); in AlignmentEndPosition()
670 p += bam_cigar_oplen(c[i]); in NumSoftClip()
680 p += bam_cigar_oplen(c[i]); in NumHardClip()
[all …]
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| /dports/biology/py-pysam/pysam-0.18.0/samtools/ |
| H A D | bam_ampliconclip.c | 331 hardclip += bam_cigar_oplen(orig_cigar[i]); in bam_trim_left()
334 if (bam_cigar_oplen(orig_cigar[i]) <= ref_remove) { in bam_trim_left()
335 ref_remove -= bam_cigar_oplen(orig_cigar[i]); in bam_trim_left()
339 new_pos += bam_cigar_oplen(orig_cigar[i]); in bam_trim_left()
342 qry_removed += bam_cigar_oplen(orig_cigar[i]); in bam_trim_left()
375 && bam_cigar_oplen(orig_cigar[i]) > ref_remove) { in bam_trim_left()
480 hardclip += bam_cigar_oplen(orig_cigar[i]); in bam_trim_right()
484 ref_remove -= bam_cigar_oplen(orig_cigar[i]); in bam_trim_right()
490 qry_removed += bam_cigar_oplen(orig_cigar[i]); in bam_trim_right()
573 len += bam_cigar_oplen(cigar[i]); in active_query_len()
[all …]
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| H A D | bam_ampliconclip.c.pysam.c | 333 hardclip += bam_cigar_oplen(orig_cigar[i]); in bam_trim_left()
336 if (bam_cigar_oplen(orig_cigar[i]) <= ref_remove) { in bam_trim_left()
337 ref_remove -= bam_cigar_oplen(orig_cigar[i]); in bam_trim_left()
341 new_pos += bam_cigar_oplen(orig_cigar[i]); in bam_trim_left()
344 qry_removed += bam_cigar_oplen(orig_cigar[i]); in bam_trim_left()
377 && bam_cigar_oplen(orig_cigar[i]) > ref_remove) { in bam_trim_left()
482 hardclip += bam_cigar_oplen(orig_cigar[i]); in bam_trim_right()
486 ref_remove -= bam_cigar_oplen(orig_cigar[i]); in bam_trim_right()
492 qry_removed += bam_cigar_oplen(orig_cigar[i]); in bam_trim_right()
575 len += bam_cigar_oplen(cigar[i]); in active_query_len()
[all …]
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| H A D | bam.c | 92 int len = bam_cigar_oplen(cigar[k]); in bam_remove_B()
99 int len1 = bam_cigar_oplen(new_cigar[t]); in bam_remove_B()
107 if (bam_cigar_oplen(new_cigar[t]) == 0) --t; // squeeze out the zero-length operation in bam_remove_B()
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| H A D | bam.c.pysam.c | 94 int len = bam_cigar_oplen(cigar[k]); in bam_remove_B()
101 int len1 = bam_cigar_oplen(new_cigar[t]); in bam_remove_B()
109 if (bam_cigar_oplen(new_cigar[t]) == 0) --t; // squeeze out the zero-length operation in bam_remove_B()
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| H A D | bam_mate.c | 59 kputw(bam_cigar_oplen(cigar[i]), str); in bam_template_cigar()
68 kputw(bam_cigar_oplen(cigar[i]), str); in bam_template_cigar()
175 if (kputw(bam_cigar_oplen(cigar[i]), str) == EOF) return -1; in bam_format_cigar()
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| H A D | bam_mate.c.pysam.c | 61 kputw(bam_cigar_oplen(cigar[i]), str); in bam_template_cigar()
70 kputw(bam_cigar_oplen(cigar[i]), str); in bam_template_cigar()
177 if (kputw(bam_cigar_oplen(cigar[i]), str) == EOF) return -1; in bam_format_cigar()
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| H A D | bam2depth.c | 135 l -= bam_cigar_oplen(cigar[kl]); in qlen_used()
141 l -= bam_cigar_oplen(cigar[kr]); in qlen_used()
153 l += bam_cigar_oplen(cigar[k]); in qlen_used()
342 int oplen = bam_cigar_oplen(cig[j]); in add_depth()
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| H A D | bam2depth.c.pysam.c | 137 l -= bam_cigar_oplen(cigar[kl]); in qlen_used()
143 l -= bam_cigar_oplen(cigar[kr]); in qlen_used()
155 l += bam_cigar_oplen(cigar[k]); in qlen_used()
344 int oplen = bam_cigar_oplen(cig[j]); in add_depth()
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| H A D | padding.c | 104 ol = bam_cigar_oplen(cigar[k]); in unpad_seq()
338 … cigar2[i] = bam_cigar_gen(bam_cigar_oplen(cigar2[i-2]) + bam_cigar_oplen(cigar2[i]), post_op); in bam_pad2unpad()
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| H A D | padding.c.pysam.c | 106 ol = bam_cigar_oplen(cigar[k]); in unpad_seq()
340 … cigar2[i] = bam_cigar_gen(bam_cigar_oplen(cigar2[i-2]) + bam_cigar_oplen(cigar2[i]), post_op); in bam_pad2unpad()
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| /dports/biology/samtools/samtools-1.14/ |
| H A D | bam_ampliconclip.c | 331 hardclip += bam_cigar_oplen(orig_cigar[i]); in bam_trim_left()
334 if (bam_cigar_oplen(orig_cigar[i]) <= ref_remove) { in bam_trim_left()
335 ref_remove -= bam_cigar_oplen(orig_cigar[i]); in bam_trim_left()
339 new_pos += bam_cigar_oplen(orig_cigar[i]); in bam_trim_left()
342 qry_removed += bam_cigar_oplen(orig_cigar[i]); in bam_trim_left()
375 && bam_cigar_oplen(orig_cigar[i]) > ref_remove) { in bam_trim_left()
480 hardclip += bam_cigar_oplen(orig_cigar[i]); in bam_trim_right()
484 ref_remove -= bam_cigar_oplen(orig_cigar[i]); in bam_trim_right()
490 qry_removed += bam_cigar_oplen(orig_cigar[i]); in bam_trim_right()
573 len += bam_cigar_oplen(cigar[i]); in active_query_len()
[all …]
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| H A D | bam.c | 92 int len = bam_cigar_oplen(cigar[k]); in bam_remove_B()
99 int len1 = bam_cigar_oplen(new_cigar[t]); in bam_remove_B()
107 if (bam_cigar_oplen(new_cigar[t]) == 0) --t; // squeeze out the zero-length operation in bam_remove_B()
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| H A D | bam_mate.c | 59 kputw(bam_cigar_oplen(cigar[i]), str); in bam_template_cigar()
68 kputw(bam_cigar_oplen(cigar[i]), str); in bam_template_cigar()
175 if (kputw(bam_cigar_oplen(cigar[i]), str) == EOF) return -1; in bam_format_cigar()
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| H A D | bam2depth.c | 135 l -= bam_cigar_oplen(cigar[kl]); in qlen_used()
141 l -= bam_cigar_oplen(cigar[kr]); in qlen_used()
153 l += bam_cigar_oplen(cigar[k]); in qlen_used()
342 int oplen = bam_cigar_oplen(cig[j]); in add_depth()
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| H A D | padding.c | 104 ol = bam_cigar_oplen(cigar[k]); in unpad_seq()
338 … cigar2[i] = bam_cigar_gen(bam_cigar_oplen(cigar2[i-2]) + bam_cigar_oplen(cigar2[i]), post_op); in bam_pad2unpad()
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| /dports/biology/vt/vt-0.57721/ |
| H A D | augmented_bam_record.cpp | 79 oplen = bam_cigar_oplen(cigar[i]); in initialize()
281 uint32_t oplen = bam_cigar_oplen(aug_cigar[i]); in initialize()
389 int32_t oplen = bam_cigar_oplen(aug_cigar[i]); in print()
432 int32_t oplen = bam_cigar_oplen(aug_cigar[i]); in print()
453 oplen = bam_cigar_oplen(aug_cigar[i]); in print()
470 oplen = bam_cigar_oplen(aug_cigar[i]); in print()
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| H A D | read_filter.cpp | 149 int32_t oplen = bam_cigar_oplen(cigar[i]); in filter_read()
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| H A D | bcf_genotyping_buffered_reader.cpp | 643 uint32_t oplen = bam_cigar_oplen(aug_cigar[i]); in collect_sufficient_statistics()
773 uint32_t oplen = bam_cigar_oplen(aug_cigar[i]); in collect_sufficient_statistics()
935 uint32_t oplen = bam_cigar_oplen(aug_cigar[i]); in collect_sufficient_statistics()
1220 uint32_t oplen = bam_cigar_oplen(aug_cigar[i]); in collect_sufficient_statistics()
1485 uint32_t oplen = bam_cigar_oplen(aug_cigar[i]); in collect_sufficient_statistics()
1612 uint32_t oplen = bam_cigar_oplen(aug_cigar[i]); in collect_sufficient_statistics()
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| /dports/biology/freebayes/freebayes-1.3.5/contrib/SeqLib/src/ |
| H A D | BamRecord.cpp | 661 out << bam_cigar_oplen(c.data) << bam_cigar_opchr(c.data); in operator <<()
725 for (size_t j = 0; j < bam_cigar_oplen(c[k]); ++j) in OverlappingCoverage()
728 pos = pos + bam_cigar_oplen(c[k]); in OverlappingCoverage()
735 for (size_t j = 0; j < bam_cigar_oplen(c2[k]); ++j) in OverlappingCoverage()
739 pos = pos + bam_cigar_oplen(c2[k]); in OverlappingCoverage()
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| /dports/biology/pbbam/pbbam-0.18.0/tests/src/ |
| H A D | test_LongCigar.cpp | 78 EXPECT_EQ(expectedLength, bam_cigar_oplen(op)); in CheckLongCigarTag()
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| /dports/biology/star/STAR-2.7.9a/source/ |
| H A D | BAMfunctions.cpp | 14 cigarString+=to_string((uint)bam_cigar_oplen(cigar[i]))+bam_cigar_opchr(cigar[i]); in bam_cigarString()
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| /dports/biology/pbbam/pbbam-0.18.0/src/ |
| H A D | BamRecordImpl.cpp | 33 const uint32_t length = bam_cigar_oplen(src[i]); in FetchRawCigar()
50 static_cast<int32_t>(bam_cigar_oplen(firstCigarOp)) != c->l_qseq) { in HasLongCigar()
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| /dports/biology/bcftools/bcftools-1.14/ |
| H A D | bam2bcf_indel.c | 112 slen -= bam_cigar_oplen(cigar[k]); in get_pos()
115 sc_len += bam_cigar_oplen(cigar[k]); in get_pos()
121 int srlen = bam_cigar_oplen(cigar[k]); in get_pos()
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| /dports/biology/bio-mocha/bcftools-1.14/ |
| H A D | bam2bcf_indel.c | 112 slen -= bam_cigar_oplen(cigar[k]); in get_pos()
115 sc_len += bam_cigar_oplen(cigar[k]); in get_pos()
121 int srlen = bam_cigar_oplen(cigar[k]); in get_pos()
|