* samtools-0.1.9-1 (r786)

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index f0e63ce62cd91cc6cada955eaa19c9b2493e1872..c23726ec51272658f1c7b876d0822085a57ea2b7 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -183,10 +183,15 @@ static inline void pileup_seq(const bam_pileup1_t *p, int pos, int ref_len, cons
                putchar(p->b->core.qual > 93? 126 : p->b->core.qual + 33);
        }
        if (!p->is_del) {
-               int rb, c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
-               rb = (ref && pos < ref_len)? ref[pos] : 'N';
-               if (c == '=' || toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
-               else c = bam1_strand(p->b)? tolower(c) : toupper(c);
+               int c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
+               if (ref) {
+                       int rb = pos < ref_len? ref[pos] : 'N';
+                       if (c == '=' || bam_nt16_table[c] == bam_nt16_table[rb]) c = bam1_strand(p->b)? ',' : '.';
+                       else c = bam1_strand(p->b)? tolower(c) : toupper(c);
+               } else {
+                       if (c == '=') c = bam1_strand(p->b)? ',' : '.';
+                       else c = bam1_strand(p->b)? tolower(c) : toupper(c);
+               }
                putchar(c);
        } else putchar(p->is_refskip? (bam1_strand(p->b)? '<' : '>') : '*');
        if (p->indel > 0) {
@@ -286,16 +291,18 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
        }
        // print pileup sequences
        printw(n, stdout); putchar('\t');
-       rms_aux = 0; // we need to recalculate rms_mapq when -c is not flagged on the command line
-       for (i = 0; i < n; ++i) {
-               const bam_pileup1_t *p = pu + i;
-               int tmp = p->b->core.qual < d->c->cap_mapQ? p->b->core.qual : d->c->cap_mapQ;
-               rms_aux += tmp * tmp;
-               pileup_seq(p, pos, d->len, d->ref);
-       }
+       for (i = 0; i < n; ++i)
+               pileup_seq(pu + i, pos, d->len, d->ref);
        // finalize rms_mapq
-       rms_aux = (uint64_t)(sqrt((double)rms_aux / n) + .499);
-       if (rms_mapq < 0) rms_mapq = rms_aux;
+       if (d->format & BAM_PLF_CNS) {
+               for (i = rms_aux = 0; i < n; ++i) {
+                       const bam_pileup1_t *p = pu + i;
+                       int tmp = p->b->core.qual < d->c->cap_mapQ? p->b->core.qual : d->c->cap_mapQ;
+                       rms_aux += tmp * tmp;
+               }
+               rms_aux = (uint64_t)(sqrt((double)rms_aux / n) + .499);
+               if (rms_mapq < 0) rms_mapq = rms_aux;
+       }
        putchar('\t');
        // print quality
        for (i = 0; i < n; ++i) {
@@ -466,6 +473,7 @@ int bam_pileup(int argc, char *argv[])
                        bam_plp_set_mask(iter, d->mask);
                        while ((ret = samread(fp, b)) >= 0) {
                                int skip = 0;
+                               if ((int)b->core.tid < 0) break;
                                // update d->ref if necessary
                                if (d->fai && (int)b->core.tid != d->tid) {
                                        free(d->ref);
@@ -520,6 +528,8 @@ int bam_pileup(int argc, char *argv[])
 #define MPLP_NO_COMP 0x20
 #define MPLP_NO_ORPHAN 0x40
 #define MPLP_REALN   0x80
+#define MPLP_FMT_DP 0x100
+#define MPLP_FMT_SP 0x200
 
 typedef struct {
        int max_mq, min_mq, flag, min_baseQ, capQ_thres;
@@ -706,7 +716,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                        for (i = 0; i < gplp.n; ++i)
                                bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i);
                        bcf_call_combine(gplp.n, bcr, ref16, &bc);
-                       bcf_call2bcf(tid, pos, &bc, b);
+                       bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0, (conf->flag&MPLP_FMT_SP));
                        bcf_write(bp, bh, b);
                        bcf_destroy(b);
                } else {
@@ -761,7 +771,8 @@ int bam_mpileup(int argc, char *argv[])
        mplp.max_mq = 60;
        mplp.min_baseQ = 13;
        mplp.capQ_thres = 0;
-       while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:")) >= 0) {
+       mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN;
+       while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:BDS")) >= 0) {
                switch (c) {
                case 'f':
                        mplp.fai = fai_load(optarg);
@@ -772,8 +783,11 @@ int bam_mpileup(int argc, char *argv[])
                case 'g': mplp.flag |= MPLP_GLF; break;
                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 'C': mplp.capQ_thres = atoi(optarg); break;
                case 'M': mplp.max_mq = atoi(optarg); break;
                case 'q': mplp.min_mq = atoi(optarg); break;
@@ -791,6 +805,9 @@ int bam_mpileup(int argc, char *argv[])
                fprintf(stderr, "         -q INT      filter out alignment with MQ smaller than INT [%d]\n", mplp.min_mq);
                fprintf(stderr, "         -g          generate BCF output\n");
                fprintf(stderr, "         -u          do not compress BCF output\n");
+               fprintf(stderr, "         -B          disable BAQ computation\n");
+               fprintf(stderr, "         -D          output per-sample DP\n");
+               fprintf(stderr, "         -S          output per-sample SP (strand bias P-value, slow)\n");
                fprintf(stderr, "\n");
                fprintf(stderr, "Notes: Assuming diploid individuals.\n\n");
                return 1;