/dports/biology/stacks/stacks-2.4/htslib/cram/ |
H A D | cram_decode.c | 1340 cig_op = BAM_CMATCH; in cram_decode_seq() 1453 cig_op = BAM_CMATCH; in cram_decode_seq() 1504 cig_op = BAM_CDEL; in cram_decode_seq() 1527 cig_op = BAM_CINS; in cram_decode_seq() 1549 cig_op = BAM_CINS; in cram_decode_seq() 1595 cig_op = BAM_CMATCH; in cram_decode_seq() 1620 cig_op = BAM_CMATCH; in cram_decode_seq() 1671 cig_op = BAM_CMATCH; in cram_decode_seq() 1719 cig_op = BAM_CPAD; in cram_decode_seq() 1736 cig_op = BAM_CREF_SKIP; in cram_decode_seq() [all …]
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H A D | cram_encode.c | 2665 enum cigar_op cig_op = cig_from[i] & BAM_CIGAR_MASK; in process_one_read() local 2671 switch (cig_op) { in process_one_read() 2812 hts_log_error("Unknown CIGAR op code %d", cig_op); in process_one_read()
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/dports/biology/kallisto/kallisto-0.46.1/ext/htslib/cram/ |
H A D | cram_decode.c | 1342 cig_op = BAM_CMATCH; in cram_decode_seq() 1455 cig_op = BAM_CMATCH; in cram_decode_seq() 1506 cig_op = BAM_CDEL; in cram_decode_seq() 1529 cig_op = BAM_CINS; in cram_decode_seq() 1551 cig_op = BAM_CINS; in cram_decode_seq() 1597 cig_op = BAM_CMATCH; in cram_decode_seq() 1622 cig_op = BAM_CMATCH; in cram_decode_seq() 1673 cig_op = BAM_CMATCH; in cram_decode_seq() 1721 cig_op = BAM_CPAD; in cram_decode_seq() 1738 cig_op = BAM_CREF_SKIP; in cram_decode_seq() [all …]
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H A D | cram_encode.c | 2677 enum cigar_op cig_op = cig_from[i] & BAM_CIGAR_MASK; in process_one_read() local 2683 switch (cig_op) { in process_one_read() 2825 fprintf(stderr, "Unknown CIGAR op code %d\n", cig_op); in process_one_read()
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/dports/biology/vt/vt-0.57721/lib/htslib/cram/ |
H A D | cram_decode.c | 1345 cig_op = BAM_CMATCH; in cram_decode_seq() 1458 cig_op = BAM_CMATCH; in cram_decode_seq() 1511 cig_op = BAM_CDEL; in cram_decode_seq() 1534 cig_op = BAM_CINS; in cram_decode_seq() 1556 cig_op = BAM_CINS; in cram_decode_seq() 1604 cig_op = BAM_CMATCH; in cram_decode_seq() 1629 cig_op = BAM_CMATCH; in cram_decode_seq() 1683 cig_op = BAM_CMATCH; in cram_decode_seq() 1731 cig_op = BAM_CPAD; in cram_decode_seq() 1831 cig_op = BAM_CBASE_MATCH; in cram_decode_seq() [all …]
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H A D | cram_encode.c | 2649 enum cigar_op cig_op = cig_from[i] & BAM_CIGAR_MASK; in process_one_read() local 2655 switch (cig_op) { in process_one_read() 2800 hts_log_error("Unknown CIGAR op code %d", cig_op); in process_one_read()
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/dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/cram/ |
H A D | cram_decode.c | 1249 cig_op = BAM_CMATCH; in cram_decode_seq() 1363 cig_op = BAM_CMATCH; in cram_decode_seq() 1416 cig_op = BAM_CDEL; in cram_decode_seq() 1439 cig_op = BAM_CINS; in cram_decode_seq() 1461 cig_op = BAM_CINS; in cram_decode_seq() 1510 cig_op = BAM_CMATCH; in cram_decode_seq() 1538 cig_op = BAM_CMATCH; in cram_decode_seq() 1592 cig_op = BAM_CMATCH; in cram_decode_seq() 1643 cig_op = BAM_CPAD; in cram_decode_seq() 1749 cig_op = BAM_CBASE_MATCH; in cram_decode_seq() [all …]
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H A D | cram_encode.c | 2793 enum cigar_op cig_op = cig_from[i] & BAM_CIGAR_MASK; in process_one_read() local 2799 switch (cig_op) { in process_one_read() 2968 hts_log_error("Unknown CIGAR op code %d", cig_op); in process_one_read()
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/dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/cram/ |
H A D | cram_decode.c | 1345 cig_op = BAM_CMATCH; in cram_decode_seq() 1458 cig_op = BAM_CMATCH; in cram_decode_seq() 1511 cig_op = BAM_CDEL; in cram_decode_seq() 1534 cig_op = BAM_CINS; in cram_decode_seq() 1556 cig_op = BAM_CINS; in cram_decode_seq() 1604 cig_op = BAM_CMATCH; in cram_decode_seq() 1629 cig_op = BAM_CMATCH; in cram_decode_seq() 1683 cig_op = BAM_CMATCH; in cram_decode_seq() 1731 cig_op = BAM_CPAD; in cram_decode_seq() 1831 cig_op = BAM_CBASE_MATCH; in cram_decode_seq() [all …]
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H A D | cram_encode.c | 2649 enum cigar_op cig_op = cig_from[i] & BAM_CIGAR_MASK; in process_one_read() local 2655 switch (cig_op) { in process_one_read() 2800 hts_log_error("Unknown CIGAR op code %d", cig_op); in process_one_read()
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/dports/biology/iolib/io_lib-io_lib-1-14-10/io_lib/ |
H A D | cram_decode.c | 1426 cig_op = BAM_CMATCH; in cram_decode_seq() 1545 cig_op = BAM_CMATCH; in cram_decode_seq() 1596 cig_op = BAM_CDEL; in cram_decode_seq() 1619 cig_op = BAM_CINS; in cram_decode_seq() 1642 cig_op = BAM_CINS; in cram_decode_seq() 1688 cig_op = BAM_CMATCH; in cram_decode_seq() 1713 cig_op = BAM_CMATCH; in cram_decode_seq() 1764 cig_op = BAM_CMATCH; in cram_decode_seq() 1812 cig_op = BAM_CPAD; in cram_decode_seq() 1830 cig_op = BAM_CREF_SKIP; in cram_decode_seq() [all …]
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H A D | cram_encode.c | 2649 enum cigar_op cig_op = cig_from[i] & BAM_CIGAR_MASK; in process_one_read() local 2655 switch (cig_op) { in process_one_read() 2798 fprintf(stderr, "Unknown CIGAR op code %d\n", cig_op); in process_one_read()
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/dports/biology/py-pysam/pysam-0.18.0/htslib/cram/ |
H A D | cram_decode.c | 1250 cig_op = BAM_CMATCH; in cram_decode_seq() 1364 cig_op = BAM_CMATCH; in cram_decode_seq() 1417 cig_op = BAM_CDEL; in cram_decode_seq() 1440 cig_op = BAM_CINS; in cram_decode_seq() 1462 cig_op = BAM_CINS; in cram_decode_seq() 1511 cig_op = BAM_CMATCH; in cram_decode_seq() 1539 cig_op = BAM_CMATCH; in cram_decode_seq() 1593 cig_op = BAM_CMATCH; in cram_decode_seq() 1644 cig_op = BAM_CPAD; in cram_decode_seq() 1750 cig_op = BAM_CBASE_MATCH; in cram_decode_seq() [all …]
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H A D | cram_encode.c | 2807 enum cigar_op cig_op = cig_from[i] & BAM_CIGAR_MASK; in process_one_read() local 2813 switch (cig_op) { in process_one_read() 3020 hts_log_error("Unknown CIGAR op code %d", cig_op); in process_one_read()
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/dports/biology/htslib/htslib-1.14/cram/ |
H A D | cram_decode.c | 1250 cig_op = BAM_CMATCH; in cram_decode_seq() 1364 cig_op = BAM_CMATCH; in cram_decode_seq() 1417 cig_op = BAM_CDEL; in cram_decode_seq() 1440 cig_op = BAM_CINS; in cram_decode_seq() 1462 cig_op = BAM_CINS; in cram_decode_seq() 1511 cig_op = BAM_CMATCH; in cram_decode_seq() 1539 cig_op = BAM_CMATCH; in cram_decode_seq() 1593 cig_op = BAM_CMATCH; in cram_decode_seq() 1644 cig_op = BAM_CPAD; in cram_decode_seq() 1750 cig_op = BAM_CBASE_MATCH; in cram_decode_seq() [all …]
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H A D | cram_encode.c | 2807 enum cigar_op cig_op = cig_from[i] & BAM_CIGAR_MASK; in process_one_read() local 2813 switch (cig_op) { in process_one_read() 3020 hts_log_error("Unknown CIGAR op code %d", cig_op); in process_one_read()
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/dports/biology/py-pysam/pysam-0.18.0/samtools/ |
H A D | bam_ampliconclip.c | 295 uint32_t cig_type, cig_op; in bam_trim_left() local 327 cig_op = bam_cigar_op(orig_cigar[i]); in bam_trim_left() 328 cig_type = bam_cigar_type(cig_op); in bam_trim_left() 330 if (cig_op == BAM_CHARD_CLIP) { in bam_trim_left() 445 uint32_t cig_type, cig_op; in bam_trim_right() local 476 cig_op = bam_cigar_op(orig_cigar[i]); in bam_trim_right() 477 cig_type = bam_cigar_type(cig_op); in bam_trim_right() 479 if (cig_op == BAM_CHARD_CLIP) { in bam_trim_right() 564 uint32_t cig_type, cig_op; in active_query_len() local 569 cig_op = bam_cigar_op(cigar[i]); in active_query_len() [all …]
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H A D | bam_ampliconclip.c.pysam.c | 297 uint32_t cig_type, cig_op; in bam_trim_left() local 329 cig_op = bam_cigar_op(orig_cigar[i]); in bam_trim_left() 330 cig_type = bam_cigar_type(cig_op); in bam_trim_left() 332 if (cig_op == BAM_CHARD_CLIP) { in bam_trim_left() 447 uint32_t cig_type, cig_op; in bam_trim_right() local 478 cig_op = bam_cigar_op(orig_cigar[i]); in bam_trim_right() 479 cig_type = bam_cigar_type(cig_op); in bam_trim_right() 481 if (cig_op == BAM_CHARD_CLIP) { in bam_trim_right() 566 uint32_t cig_type, cig_op; in active_query_len() local 571 cig_op = bam_cigar_op(cigar[i]); in active_query_len() [all …]
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/dports/biology/samtools/samtools-1.14/ |
H A D | bam_ampliconclip.c | 295 uint32_t cig_type, cig_op; in bam_trim_left() local 327 cig_op = bam_cigar_op(orig_cigar[i]); in bam_trim_left() 328 cig_type = bam_cigar_type(cig_op); in bam_trim_left() 330 if (cig_op == BAM_CHARD_CLIP) { in bam_trim_left() 445 uint32_t cig_type, cig_op; in bam_trim_right() local 476 cig_op = bam_cigar_op(orig_cigar[i]); in bam_trim_right() 477 cig_type = bam_cigar_type(cig_op); in bam_trim_right() 479 if (cig_op == BAM_CHARD_CLIP) { in bam_trim_right() 564 uint32_t cig_type, cig_op; in active_query_len() local 569 cig_op = bam_cigar_op(cigar[i]); in active_query_len() [all …]
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/dports/biology/sra-tools/sra-tools-2.11.0/tools/sra-pileup/ |
H A D | cg_tools.c | 567 static size_t fmt_cigar_elem( char * dst, uint32_t cig_oplen, char cig_op ) in fmt_cigar_elem() argument 570 rc_t rc = string_printf ( dst, 11, &num_writ, "%d%c", cig_oplen, cig_op ); in fmt_cigar_elem()
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