| /dports/biology/py-pysam/pysam-0.18.0/samtools/ |
| H A D | bam_plbuf.c | 61 int ret, n_plp, tid; in bam_plbuf_push() local
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| H A D | bam_plbuf.c.pysam.c | 63 int ret, n_plp, tid; in bam_plbuf_push() local
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| H A D | bedcov.c | 75 int *n_plp, dret, i, j, m, n, c, ret, status = 0, min_mapQ = 0, skip_DN = 0; in main_bedcov() local
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| H A D | bedcov.c.pysam.c | 77 int *n_plp, dret, i, j, m, n, c, ret, status = 0, min_mapQ = 0, skip_DN = 0; in main_bedcov() local
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| H A D | bam_plcmd.c | 233 int *n_plp, *m_plp; member
443 int n, char *const*fn, int *n_plp, const bam_pileup1_t **plp, int ignore_rg) in group_smpl()
481 int i, tid, *n_plp, tid0 = 0, max_depth, max_indel_depth; in mpileup() local
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| H A D | bam_plcmd.c.pysam.c | 235 int *n_plp, *m_plp; member
445 int n, char *const*fn, int *n_plp, const bam_pileup1_t **plp, int ignore_rg) in group_smpl()
483 int i, tid, *n_plp, tid0 = 0, max_depth, max_indel_depth; in mpileup() local
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| /dports/biology/samtools/samtools-1.14/ |
| H A D | bam_plbuf.c | 61 int ret, n_plp, tid; in bam_plbuf_push() local
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| H A D | bedcov.c | 75 int *n_plp, dret, i, j, m, n, c, ret, status = 0, min_mapQ = 0, skip_DN = 0; in main_bedcov() local
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| /dports/biology/bcftools/bcftools-1.14/ |
| H A D | bam2bcf_indel.c | 161 static int *bcf_cgp_find_types(int n, int *n_plp, bam_pileup1_t **plp, in bcf_cgp_find_types()
278 static char **bcf_cgp_ref_sample(int n, int *n_plp, bam_pileup1_t **plp, in bcf_cgp_ref_sample()
432 static char *bcf_cgp_calc_cons(int n, int *n_plp, bam_pileup1_t **plp, in bcf_cgp_calc_cons()
593 static int bcf_cgp_compute_indelQ(int n, int *n_plp, bam_pileup1_t **plp, in bcf_cgp_compute_indelQ()
694 int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, in bcf_call_gap_prep()
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| H A D | mpileup.c | 93 int *n_plp; member
126 int *n_plp, *m_plp; member
347 static void group_smpl(mplp_pileup_t *m, bam_smpl_t *bsmpl, int n, int *n_plp, const bam_pileup1_t … in group_smpl()
406 static void mplp_realn(int n, int *n_plp, const bam_pileup1_t **plp, in mplp_realn()
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| /dports/biology/bio-mocha/bcftools-1.14/ |
| H A D | bam2bcf_indel.c | 161 static int *bcf_cgp_find_types(int n, int *n_plp, bam_pileup1_t **plp, in bcf_cgp_find_types()
278 static char **bcf_cgp_ref_sample(int n, int *n_plp, bam_pileup1_t **plp, in bcf_cgp_ref_sample()
432 static char *bcf_cgp_calc_cons(int n, int *n_plp, bam_pileup1_t **plp, in bcf_cgp_calc_cons()
593 static int bcf_cgp_compute_indelQ(int n, int *n_plp, bam_pileup1_t **plp, in bcf_cgp_compute_indelQ()
694 int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, in bcf_call_gap_prep()
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| H A D | mpileup.c | 93 int *n_plp; member
126 int *n_plp, *m_plp; member
347 static void group_smpl(mplp_pileup_t *m, bam_smpl_t *bsmpl, int n, int *n_plp, const bam_pileup1_t … in group_smpl()
406 static void mplp_realn(int n, int *n_plp, const bam_pileup1_t **plp, in mplp_realn()
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| /dports/biology/py-pysam/pysam-0.18.0/bcftools/ |
| H A D | bam2bcf_indel.c | 161 static int *bcf_cgp_find_types(int n, int *n_plp, bam_pileup1_t **plp, in bcf_cgp_find_types()
278 static char **bcf_cgp_ref_sample(int n, int *n_plp, bam_pileup1_t **plp, in bcf_cgp_ref_sample()
432 static char *bcf_cgp_calc_cons(int n, int *n_plp, bam_pileup1_t **plp, in bcf_cgp_calc_cons()
593 static int bcf_cgp_compute_indelQ(int n, int *n_plp, bam_pileup1_t **plp, in bcf_cgp_compute_indelQ()
694 int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, in bcf_call_gap_prep()
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| H A D | bam2bcf_indel.c.pysam.c | 163 static int *bcf_cgp_find_types(int n, int *n_plp, bam_pileup1_t **plp, in bcf_cgp_find_types()
280 static char **bcf_cgp_ref_sample(int n, int *n_plp, bam_pileup1_t **plp, in bcf_cgp_ref_sample()
434 static char *bcf_cgp_calc_cons(int n, int *n_plp, bam_pileup1_t **plp, in bcf_cgp_calc_cons()
595 static int bcf_cgp_compute_indelQ(int n, int *n_plp, bam_pileup1_t **plp, in bcf_cgp_compute_indelQ()
696 int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, in bcf_call_gap_prep()
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| H A D | mpileup.c | 93 int *n_plp; member
126 int *n_plp, *m_plp; member
347 static void group_smpl(mplp_pileup_t *m, bam_smpl_t *bsmpl, int n, int *n_plp, const bam_pileup1_t … in group_smpl()
406 static void mplp_realn(int n, int *n_plp, const bam_pileup1_t **plp, in mplp_realn()
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| H A D | mpileup.c.pysam.c | 95 int *n_plp; member
128 int *n_plp, *m_plp; member
349 static void group_smpl(mplp_pileup_t *m, bam_smpl_t *bsmpl, int n, int *n_plp, const bam_pileup1_t … in group_smpl()
408 static void mplp_realn(int n, int *n_plp, const bam_pileup1_t **plp, in mplp_realn()
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| /dports/biology/ugene/ugene-40.1/src/libs_3rdparty/samtools/src/samtools/ |
| H A D | bam_pileup.c | 199 int n_plp = 0; in bam_plp_next() local
361 int ret, n_plp, tid, pos; in bam_plbuf_push() local
378 int *n_plp; member
415 int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp) in bam_mplp_auto()
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| H A D | bam2depth.c | 38 int i, n, tid, beg, end, pos, *n_plp, baseQ = 0, mapQ = 0; in main() local
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| H A D | bam_plcmd.c | 103 int *n_plp, *m_plp; member
172 int n, char *const*fn, int *n_plp, const bam_pileup1_t **plp, int ignore_rg) in group_smpl()
203 …int i, tid, pos, *n_plp, tid0 = -1, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid = -1, max_depth, max… in mpileup() local
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| /dports/biology/stringtie/stringtie-2.1.1/samtools-0.1.18/ |
| H A D | bam_pileup.c | 199 int n_plp = 0; in bam_plp_next() local
361 int ret, n_plp, tid, pos; in bam_plbuf_push() local
378 int *n_plp; member
415 int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp) in bam_mplp_auto()
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| H A D | bam_plcmd.c | 102 int *n_plp, *m_plp; member
151 int n, char *const*fn, int *n_plp, const bam_pileup1_t **plp, int ignore_rg) in group_smpl()
182 …int i, tid, pos, *n_plp, tid0 = -1, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid = -1, max_depth, max… in mpileup() local
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| /dports/biology/seqan1/seqan-1.3.1/lib/samtools/ |
| H A D | bam_pileup.c | 199 int n_plp = 0; in bam_plp_next() local
361 int ret, n_plp, tid, pos; in bam_plbuf_push() local
378 int *n_plp; member
415 int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp) in bam_mplp_auto()
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| H A D | bam_plcmd.c | 470 int ret, tid, pos, n_plp; in bam_pileup() local
554 int *n_plp, *m_plp; member
584 int n, char *const*fn, int *n_plp, const bam_pileup1_t **plp) in group_smpl()
611 int i, tid, pos, *n_plp, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid, max_depth; in mpileup() local
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| /dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/test/ |
| H A D | pileup.c | 164 int n_plp[1] = { 0 }; in test_mpileup() local
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| /dports/biology/htslib/htslib-1.14/test/ |
| H A D | pileup.c | 164 int n_plp[1] = { 0 }; in test_mpileup() local
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