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Searched refs:cig_op (Results 1 – 20 of 20) sorted by relevance

/dports/biology/stacks/stacks-2.4/htslib/cram/
H A Dcram_decode.c1340 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 …]
H A Dcram_encode.c2665 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()
/dports/biology/kallisto/kallisto-0.46.1/ext/htslib/cram/
H A Dcram_decode.c1342 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 …]
H A Dcram_encode.c2677 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()
/dports/biology/vt/vt-0.57721/lib/htslib/cram/
H A Dcram_decode.c1345 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 …]
H A Dcram_encode.c2649 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()
/dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/cram/
H A Dcram_decode.c1249 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 …]
H A Dcram_encode.c2793 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()
/dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/cram/
H A Dcram_decode.c1345 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 …]
H A Dcram_encode.c2649 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()
/dports/biology/iolib/io_lib-io_lib-1-14-10/io_lib/
H A Dcram_decode.c1426 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 …]
H A Dcram_encode.c2649 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()
/dports/biology/py-pysam/pysam-0.18.0/htslib/cram/
H A Dcram_decode.c1250 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 …]
H A Dcram_encode.c2807 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()
/dports/biology/htslib/htslib-1.14/cram/
H A Dcram_decode.c1250 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 …]
H A Dcram_encode.c2807 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()
/dports/biology/py-pysam/pysam-0.18.0/samtools/
H A Dbam_ampliconclip.c295 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 …]
H A Dbam_ampliconclip.c.pysam.c297 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 …]
/dports/biology/samtools/samtools-1.14/
H A Dbam_ampliconclip.c295 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 …]
/dports/biology/sra-tools/sra-tools-2.11.0/tools/sra-pileup/
H A Dcg_tools.c567 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()