Release samtools-0.1.14 (r933:170)

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 368502cd44fe73dc5ceb8ad6210fc2432fe49678..fd75cec8c8841a1f174731dc2eeef603571b86d2 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -534,6 +534,7 @@ int bam_pileup(int argc, char *argv[])
 #define MPLP_FMT_SP 0x200
 #define MPLP_NO_INDEL 0x400
 #define MPLP_EXT_BAQ 0x800
+#define MPLP_ILLUMINA13 0x1000
 
 typedef struct {
        int max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth;
@@ -575,6 +576,12 @@ static int mplp_func(void *data, bam1_t *b)
                        skip = (rg && bcf_str2id(ma->conf->rghash, (const char*)(rg+1)) >= 0);
                        if (skip) continue;
                }
+               if (ma->conf->flag & MPLP_ILLUMINA13) {
+                       int i;
+                       uint8_t *qual = bam1_qual(b);
+                       for (i = 0; i < b->core.l_qseq; ++i)
+                               qual[i] = qual[i] > 31? qual[i] - 31 : 0;
+               }
                has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0;
                skip = 0;
                if (has_ref && (ma->conf->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, (ma->conf->flag & MPLP_EXT_BAQ)? 3 : 1);
@@ -872,7 +879,7 @@ int bam_mpileup(int argc, char *argv[])
        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, "Agf:r:l:M:q:Q:uaRC:BDSd:L:b:P:o:e:h:Im:F:EG:")) >= 0) {
+       while ((c = getopt(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:L:b:P:o:e:h:Im:F:EG:6")) >= 0) {
                switch (c) {
                case 'f':
                        mplp.fai = fai_load(optarg);
@@ -891,6 +898,7 @@ int bam_mpileup(int argc, char *argv[])
                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 '6': mplp.flag |= MPLP_ILLUMINA13; 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;
@@ -936,6 +944,7 @@ int bam_mpileup(int argc, char *argv[])
                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, "         -G FILE     exclude read groups listed in FILE [null]\n");
+               fprintf(stderr, "         -6          quality is in the Illumina-1.3+ encoding\n");
                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");