* samtools-0.1.12-6 (r887)

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 002297a1229678a256e9045f420b89d5f273b1ea..27f67629337b89385080e1904deb80e4dd313d50 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -533,10 +533,12 @@ int bam_pileup(int argc, char *argv[])
 #define MPLP_FMT_DP 0x100
 #define MPLP_FMT_SP 0x200
 #define MPLP_NO_INDEL 0x400
+#define MPLP_EXT_BAQ 0x800
 
 typedef struct {
        int max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth;
-       int openQ, extQ, tandemQ;
+       int openQ, extQ, tandemQ, min_support; // for indels
+       double min_frac; // for indels
        char *reg, *fn_pos, *pl_list;
        faidx_t *fai;
        kh_64_t *hash;
@@ -568,7 +570,7 @@ static int mplp_func(void *data, bam1_t *b)
                if (ret < 0) break;
                has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0;
                skip = 0;
-               if (has_ref && (ma->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, 1);
+               if (has_ref && (ma->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, (ma->flag & MPLP_EXT_BAQ)? 3 : 1);
                if (has_ref && ma->capQ_thres > 10) {
                        int q = bam_cap_mapQ(b, ma->ref, ma->capQ_thres);
                        if (q < 0) skip = 1;
@@ -702,6 +704,8 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                bcr = calloc(sm->n, sizeof(bcf_callret1_t));
                bca->rghash = rghash;
                bca->openQ = conf->openQ, bca->extQ = conf->extQ, bca->tandemQ = conf->tandemQ;
+               bca->min_frac = conf->min_frac;
+               bca->min_support = conf->min_support;
        }
        ref_tid = -1; ref = 0;
        iter = bam_mplp_init(n, mplp_func, (void**)data);
@@ -850,7 +854,7 @@ int bam_mpileup(int argc, char *argv[])
        int c;
     const char *file_list = NULL;
     char **fn = NULL;
-    int nfiles = 0;
+    int nfiles = 0, use_orphan = 0;
        mplp_conf_t mplp;
        memset(&mplp, 0, sizeof(mplp_conf_t));
        mplp.max_mq = 60;
@@ -858,8 +862,9 @@ int bam_mpileup(int argc, char *argv[])
        mplp.capQ_thres = 0;
        mplp.max_depth = 250;
        mplp.openQ = 40; mplp.extQ = 20; mplp.tandemQ = 100;
+       mplp.min_frac = 0.002; mplp.min_support = 1;
        mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN;
-       while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:BDSd:b:P:o:e:h:I")) >= 0) {
+       while ((c = getopt(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:b:P:o:e:h:Im:F:E")) >= 0) {
                switch (c) {
                case 'f':
                        mplp.fai = fai_load(optarg);
@@ -873,11 +878,11 @@ int bam_mpileup(int argc, char *argv[])
                case 'u': mplp.flag |= MPLP_NO_COMP | MPLP_GLF; break;
                case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN; break;
                case 'B': mplp.flag &= ~MPLP_REALN & ~MPLP_NO_ORPHAN; break;
-               case 'O': mplp.flag |= MPLP_NO_ORPHAN; break;
                case 'R': mplp.flag |= MPLP_REALN; break;
                case 'D': mplp.flag |= MPLP_FMT_DP; break;
                case 'S': mplp.flag |= MPLP_FMT_SP; break;
                case 'I': mplp.flag |= MPLP_NO_INDEL; break;
+               case 'E': mplp.flag |= MPLP_EXT_BAQ; break;
                case 'C': mplp.capQ_thres = atoi(optarg); break;
                case 'M': mplp.max_mq = atoi(optarg); break;
                case 'q': mplp.min_mq = atoi(optarg); break;
@@ -886,8 +891,12 @@ int bam_mpileup(int argc, char *argv[])
                case 'o': mplp.openQ = atoi(optarg); break;
                case 'e': mplp.extQ = atoi(optarg); break;
                case 'h': mplp.tandemQ = atoi(optarg); break;
+               case 'A': use_orphan = 1; break;
+               case 'F': mplp.min_frac = atof(optarg); break;
+               case 'm': mplp.min_support = atoi(optarg); break;
                }
        }
+       if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN;
        if (argc == 1) {
                fprintf(stderr, "\n");
                fprintf(stderr, "Usage:   samtools mpileup [options] in1.bam [in2.bam [...]]\n\n");
@@ -903,6 +912,9 @@ int bam_mpileup(int argc, char *argv[])
                fprintf(stderr, "         -o INT      Phred-scaled gap open sequencing error probability [%d]\n", mplp.openQ);
                fprintf(stderr, "         -e INT      Phred-scaled gap extension seq error probability [%d]\n", mplp.extQ);
                fprintf(stderr, "         -h INT      coefficient for homopolyer errors [%d]\n", mplp.tandemQ);
+               fprintf(stderr, "         -m INT      minimum gapped reads for indel candidates [%d]\n", mplp.min_support);
+               fprintf(stderr, "         -F FLOAT    minimum fraction of gapped reads for candidates [%g]\n", mplp.min_frac);
+               fprintf(stderr, "         -A          use anomalous read pairs in SNP/INDEL calling\n");
                fprintf(stderr, "         -g          generate BCF output\n");
                fprintf(stderr, "         -u          do not compress BCF output\n");
                fprintf(stderr, "         -B          disable BAQ computation\n");