| /dports/biology/seqan1/seqan-1.3.1/lib/samtools/misc/ |
| H A D | export2sam.pl | 117 SAM_POS => 3, constant
243 my $x1 = ($s1[SAM_FLAG] & 0x10)? $s1[SAM_POS] + length($s1[SAM_SEQ]) : $s1[SAM_POS];
244 my $x2 = ($s2[SAM_FLAG] & 0x10)? $s2[SAM_POS] + length($s2[SAM_SEQ]) : $s2[SAM_POS];
252 $sa->[SAM_MPOS] = $sb->[SAM_POS];
332 $s->[SAM_POS] = $has_coor? $t[EXPORT_POS] : 0;
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| /dports/biology/samtools/samtools-1.14/misc/ |
| H A D | export2sam.pl | 168 SAM_POS => 3, constant
316 my $x1 = ($s1[SAM_FLAG] & 0x10)? $s1[SAM_POS] + length($s1[SAM_SEQ]) : $s1[SAM_POS];
317 my $x2 = ($s2[SAM_FLAG] & 0x10)? $s2[SAM_POS] + length($s2[SAM_SEQ]) : $s2[SAM_POS];
325 $sa->[SAM_MPOS] = $sb->[SAM_POS];
416 $s->[SAM_POS] = $has_coor? $t[EXPORT_POS] : 0;
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| /dports/biology/iolib/io_lib-io_lib-1-14-10/progs/ |
| H A D | cram_index.c | 64 SAM_RNAME | SAM_POS | SAM_CIGAR); in main()
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| H A D | scram_test.c | 257 if (col & SAM_POS) in main()
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| /dports/biology/plink/plink-ng-79b2df8c/1.9/ |
| H A D | hts.h | 131 SAM_POS = 0x00000008, enumerator
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| /dports/biology/kallisto/kallisto-0.46.1/ext/htslib/htslib/ |
| H A D | hts.h | 195 SAM_POS = 0x00000008, enumerator
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| /dports/biology/vt/vt-0.57721/lib/htslib/htslib/ |
| H A D | hts.h | 197 SAM_POS = 0x00000008, enumerator
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| /dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/htslib/ |
| H A D | hts.h | 198 SAM_POS = 0x00000008, enumerator
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| /dports/biology/stacks/stacks-2.4/htslib/htslib/ |
| H A D | hts.h | 197 SAM_POS = 0x00000008, enumerator
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| /dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/htslib/ |
| H A D | hts.h | 278 SAM_POS = 0x00000008, enumerator
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| /dports/biology/py-pysam/pysam-0.18.0/htslib/htslib/ |
| H A D | hts.h | 282 SAM_POS = 0x00000008, enumerator
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| /dports/biology/htslib/htslib-1.14/htslib/ |
| H A D | hts.h | 282 SAM_POS = 0x00000008, enumerator
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| /dports/biology/vt/vt-0.57721/lib/htslib/cram/ |
| H A D | cram_index.c | 592 cram_set_option(fd, CRAM_OPT_REQUIRED_FIELDS, SAM_RNAME | SAM_POS | SAM_CIGAR); in cram_index_build()
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| /dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/cram/ |
| H A D | cram_index.c | 592 cram_set_option(fd, CRAM_OPT_REQUIRED_FIELDS, SAM_RNAME | SAM_POS | SAM_CIGAR); in cram_index_build()
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| /dports/biology/iolib/io_lib-io_lib-1-14-10/io_lib/ |
| H A D | cram_structs.h | 884 SAM_POS = 0x00000008, enumerator
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| /dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/cram/ |
| H A D | cram_index.c | 744 cram_set_option(fd, CRAM_OPT_REQUIRED_FIELDS, SAM_RNAME | SAM_POS | SAM_CIGAR); in cram_index_build()
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| H A D | cram_io.c | 4850 fd->required_fields |= SAM_POS; in cram_set_voption()
4867 fd->required_fields |= SAM_POS; in cram_set_voption()
4943 fd->required_fields |= SAM_POS; in cram_set_voption()
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| /dports/biology/py-pysam/pysam-0.18.0/htslib/cram/ |
| H A D | cram_index.c | 744 cram_set_option(fd, CRAM_OPT_REQUIRED_FIELDS, SAM_RNAME | SAM_POS | SAM_CIGAR); in cram_index_build()
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| /dports/biology/py-pysam/pysam-0.18.0/samtools/ |
| H A D | coverage.c | 469 rf = SAM_FLAG | SAM_RNAME | SAM_POS | SAM_MAPQ | SAM_CIGAR | SAM_SEQ; in main_coverage()
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| H A D | coverage.c.pysam.c | 471 rf = SAM_FLAG | SAM_RNAME | SAM_POS | SAM_MAPQ | SAM_CIGAR | SAM_SEQ; in main_coverage()
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| H A D | bam2depth.c | 892 SAM_FLAG | SAM_RNAME | SAM_POS | SAM_CIGAR in main_depth()
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| H A D | bam2depth.c.pysam.c | 894 SAM_FLAG | SAM_RNAME | SAM_POS | SAM_CIGAR in main_depth()
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| /dports/biology/samtools/samtools-1.14/ |
| H A D | coverage.c | 469 rf = SAM_FLAG | SAM_RNAME | SAM_POS | SAM_MAPQ | SAM_CIGAR | SAM_SEQ; in main_coverage()
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| H A D | bam2depth.c | 892 SAM_FLAG | SAM_RNAME | SAM_POS | SAM_CIGAR in main_depth()
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| /dports/biology/htslib/htslib-1.14/cram/ |
| H A D | cram_index.c | 744 cram_set_option(fd, CRAM_OPT_REQUIRED_FIELDS, SAM_RNAME | SAM_POS | SAM_CIGAR); in cram_index_build()
|