/dports/biology/py-pysam/pysam-0.18.0/samtools/ |
H A D | bam_color.c | 54 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 D | bam_color.c.pysam.c | 56 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 D | bam2bcf_indel.c | 96 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 D | bam2bcf_indel.c.pysam.c | 98 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 D | bam_color.c | 54 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 D | bam2bcf_indel.c | 96 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 D | scram_pileup.c | 142 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 D | bam.c | 22 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 D | sam.h | 81 #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 D | sam.h | 81 #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 D | sam.h | 81 #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 D | sam.h | 78 #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 D | bam.c | 22 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 D | bam2bcf_indel.c | 67 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 D | bam.h | 132 #define BAM_CIGAR_MASK ((1 << BAM_CIGAR_SHIFT) - 1) macro
|
/dports/biology/stringtie/stringtie-2.1.1/samtools-0.1.18/ |
H A D | bam.c | 22 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 D | bamlite.h | 48 #define BAM_CIGAR_MASK ((1 << BAM_CIGAR_SHIFT) - 1) macro
|
/dports/biology/hisat2/hisat2-2.2.1/li_hla/ |
H A D | alignments.hpp | 105 int op = rawCigar[i] & BAM_CIGAR_MASK ; in Next()
|
/dports/biology/emboss/EMBOSS-6.6.0/ajax/core/ |
H A D | ajseqbam.h | 157 #define BAM_CIGAR_MASK ((1 << BAM_CIGAR_SHIFT) - 1) macro
|
/dports/biology/gffread/gffread-0.12.7/gclib/ |
H A D | GBam.cpp | 5 #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 D | BamConstants.h | 71 const int BAM_CIGAR_MASK = ((1 << BAM_CIGAR_SHIFT) - 1); variable
|
/dports/biology/py-pysam/pysam-0.18.0/pysam/ |
H A D | libcalignedsegment.pyx | 458 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 D | sam.h | 107 #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 D | sam.h | 107 #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 D | sam.h | 107 #define BAM_CIGAR_MASK 0xf macro 116 #define bam_cigar_op(c) ((c)&BAM_CIGAR_MASK)
|