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Searched refs:BAM_CIGAR_MASK (Results 1 – 25 of 76) sorted by relevance

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/dports/biology/py-pysam/pysam-0.18.0/samtools/
H A Dbam_color.c54 if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { in bam_aux_getCSi()
83 if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { in bam_aux_getCQi()
144 if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { in bam_aux_getCEi()
H A Dbam_color.c.pysam.c56 if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { in bam_aux_getCSi()
85 if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { in bam_aux_getCQi()
146 if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { in bam_aux_getCEi()
H A Dbam2bcf_indel.c96 int op = cigar[k] & BAM_CIGAR_MASK; in tpos2qpos()
395 if ((cigar[kk]&BAM_CIGAR_MASK) == BAM_CREF_SKIP) break; in bcf_call_gap_prep()
H A Dbam2bcf_indel.c.pysam.c98 int op = cigar[k] & BAM_CIGAR_MASK; in tpos2qpos()
397 if ((cigar[kk]&BAM_CIGAR_MASK) == BAM_CREF_SKIP) break; in bcf_call_gap_prep()
/dports/biology/samtools/samtools-1.14/
H A Dbam_color.c54 if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { in bam_aux_getCSi()
83 if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { in bam_aux_getCQi()
144 if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { in bam_aux_getCEi()
H A Dbam2bcf_indel.c96 int op = cigar[k] & BAM_CIGAR_MASK; in tpos2qpos()
395 if ((cigar[kk]&BAM_CIGAR_MASK) == BAM_CREF_SKIP) break; in bcf_call_gap_prep()
/dports/biology/iolib/io_lib-io_lib-1-14-10/progs/
H A Dscram_pileup.c142 op=p->cigar_op = p->b_cigar[p->cigar_ind] & BAM_CIGAR_MASK; in get_next_base()
190 op=p->cigar_op = p->b_cigar[p->cigar_ind] & BAM_CIGAR_MASK; in get_next_base()
300 op=p->cigar_op = p->b_cigar[p->cigar_ind] & BAM_CIGAR_MASK; in get_next_base()
520 if ((p->b_cigar[0] & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { in pileup_loop()
523 if ((p->b_cigar[1] & BAM_CIGAR_MASK) == BAM_CSOFT_CLIP) { in pileup_loop()
532 if ((p->b_cigar[0] & BAM_CIGAR_MASK) == BAM_CSOFT_CLIP) { in pileup_loop()
/dports/biology/seqan1/seqan-1.3.1/lib/samtools/
H A Dbam.c22 int op = cigar[k] & BAM_CIGAR_MASK; in bam_calend()
34 int op = cigar[k] & BAM_CIGAR_MASK; in bam_cigar2qlen()
258 kputc("MIDNSHP"[bam1_cigar(b)[i]&BAM_CIGAR_MASK], &str); in bam_format1_core()
/dports/biology/vt/vt-0.57721/lib/htslib/htslib/
H A Dsam.h81 #define BAM_CIGAR_MASK 0xf macro
84 #define bam_cigar_op(c) ((c)&BAM_CIGAR_MASK)
/dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/htslib/
H A Dsam.h81 #define BAM_CIGAR_MASK 0xf macro
84 #define bam_cigar_op(c) ((c)&BAM_CIGAR_MASK)
/dports/biology/stacks/stacks-2.4/htslib/htslib/
H A Dsam.h81 #define BAM_CIGAR_MASK 0xf macro
84 #define bam_cigar_op(c) ((c)&BAM_CIGAR_MASK)
/dports/biology/kallisto/kallisto-0.46.1/ext/htslib/htslib/
H A Dsam.h78 #define BAM_CIGAR_MASK 0xf macro
81 #define bam_cigar_op(c) ((c)&BAM_CIGAR_MASK)
/dports/biology/ugene/ugene-40.1/src/libs_3rdparty/samtools/src/samtools/
H A Dbam.c22 int op = cigar[k] & BAM_CIGAR_MASK; in bam_calend()
34 int op = cigar[k] & BAM_CIGAR_MASK; in bam_cigar2qlen()
271 kputc("MIDNSHP=X"[bam1_cigar(b)[i]&BAM_CIGAR_MASK], &str); in bam_format1_core()
H A Dbam2bcf_indel.c67 int op = cigar[k] & BAM_CIGAR_MASK; in tpos2qpos()
333 if ((cigar[kk]&BAM_CIGAR_MASK) == BAM_CREF_SKIP) break; in bcf_call_gap_prep()
H A Dbam.h132 #define BAM_CIGAR_MASK ((1 << BAM_CIGAR_SHIFT) - 1) macro
/dports/biology/stringtie/stringtie-2.1.1/samtools-0.1.18/
H A Dbam.c22 int op = cigar[k] & BAM_CIGAR_MASK; in bam_calend()
34 int op = cigar[k] & BAM_CIGAR_MASK; in bam_cigar2qlen()
271 kputc("MIDNSHP=X"[bam1_cigar(b)[i]&BAM_CIGAR_MASK], &str); in bam_format1_core()
/dports/biology/bwa/bwa-0.7.17/
H A Dbamlite.h48 #define BAM_CIGAR_MASK ((1 << BAM_CIGAR_SHIFT) - 1) macro
/dports/biology/hisat2/hisat2-2.2.1/li_hla/
H A Dalignments.hpp105 int op = rawCigar[i] & BAM_CIGAR_MASK ; in Next()
/dports/biology/emboss/EMBOSS-6.6.0/ajax/core/
H A Dajseqbam.h157 #define BAM_CIGAR_MASK ((1 << BAM_CIGAR_SHIFT) - 1) macro
/dports/biology/gffread/gffread-0.12.7/gclib/
H A DGBam.cpp5 #define _cigOp(c) ((c)&BAM_CIGAR_MASK)
481 kputc("MIDNSHP=X"[bam1_cigar(b)[i]&BAM_CIGAR_MASK], &str); in cigar()
/dports/biology/bamtools/bamtools-2.5.2/src/api/
H A DBamConstants.h71 const int BAM_CIGAR_MASK = ((1 << BAM_CIGAR_SHIFT) - 1); variable
/dports/biology/py-pysam/pysam-0.18.0/pysam/
H A Dlibcalignedsegment.pyx458 op = cigar_p[k] & BAM_CIGAR_MASK
488 op = cigar_p[k] & BAM_CIGAR_MASK
508 op = cigar_p[k] & BAM_CIGAR_MASK
528 op = cigar_p[k] & BAM_CIGAR_MASK
538 op = cigar_p[k] & BAM_CIGAR_MASK
665 op = cigar_p[k] & BAM_CIGAR_MASK
752 op = cigar_p[k] & BAM_CIGAR_MASK
875 op = cigar_p[k] & BAM_CIGAR_MASK
1783 op = cigar_p[k] & BAM_CIGAR_MASK
1922 op = cigar_p[k] & BAM_CIGAR_MASK
[all …]
/dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/htslib/
H A Dsam.h107 #define BAM_CIGAR_MASK 0xf macro
116 #define bam_cigar_op(c) ((c)&BAM_CIGAR_MASK)
/dports/biology/py-pysam/pysam-0.18.0/htslib/htslib/
H A Dsam.h107 #define BAM_CIGAR_MASK 0xf macro
116 #define bam_cigar_op(c) ((c)&BAM_CIGAR_MASK)
/dports/biology/htslib/htslib-1.14/htslib/
H A Dsam.h107 #define BAM_CIGAR_MASK 0xf macro
116 #define bam_cigar_op(c) ((c)&BAM_CIGAR_MASK)

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