* samtools-0.1.4-3 (r324)

 * make maqcns generate the correct call in repetitive regions.
 * allow filtering on mapQ at the pileup command line

diff --git a/bam_maqcns.c b/bam_maqcns.c
index 95cd2b5f68f748f1412a8dc089784f3069d972c5..44eed4e468bcbad77923719ac486966e4eaef457 100644 (file)
--- a/bam_maqcns.c
+++ b/bam_maqcns.c
@@ -213,6 +213,28 @@ glf1_t *bam_maqcns_glfgen(int _n, const bam_pileup1_t *pl, uint8_t ref_base, bam
                        if (p[j<<2|k] < 0.0) p[j<<2|k] = 0.0;
        }
 
+       { // fix p[k<<2|k]
+               float max1, max2, min;
+               int max_k, min_k;
+               max_k = min_k = -1;
+               max1 = max2 = -1.0; min = 1e30;
+               for (k = 0; k < 4; ++k) {
+                       if (b->esum[k] > max1) {
+                               max2 = max1; max1 = b->esum[k]; max_k = k;
+                       } else if (b->esum[k] > max2) {
+                               max2 = b->esum[k];
+                       }
+               }
+               for (k = 0; k < 4; ++k) {
+                       if (min > p[k<<2|k]) {
+                               min = p[k<<2|k];
+                               min_k = k;
+                       }
+               }
+               if (max1 > max2 && min_k != max_k)
+                       p[max_k<<2|max_k] = min > 1.0? min - 1.0 : 0.0;
+       }
+
        // convert necessary information to glf1_t
        g->ref_base = ref_base; g->max_mapQ = b->rms_mapQ;
        g->depth = n > 16777215? 16777215 : n;

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 46f078a99e715a89ccc4f73119192fe8d1ef280c..96f5c459df9dd88aa35d69a361898739016875d8 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -26,7 +26,7 @@ typedef struct {
        khash_t(64) *hash;
        uint32_t format;
        int tid, len, last_pos;
-       int mask;
+       int mask, min_mapQ;
        char *ref;
        glfFile fp_glf; // for glf output only
 } pu_data_t;
@@ -280,7 +280,7 @@ int bam_pileup(int argc, char *argv[])
        d->tid = -1; d->mask = BAM_DEF_MASK;
        d->c = bam_maqcns_init();
        d->ido = bam_maqindel_opt_init();
-       while ((c = getopt(argc, argv, "st:f:cT:N:r:l:im:gI:G:vM:")) >= 0) {
+       while ((c = getopt(argc, argv, "st:f:cT:N:r:l:im:gI:G:vM:q:")) >= 0) {
                switch (c) {
                case 's': d->format |= BAM_PLF_SIMPLE; break;
                case 't': fn_list = strdup(optarg); break;
@@ -297,6 +297,7 @@ int bam_pileup(int argc, char *argv[])
                case 'g': d->format |= BAM_PLF_GLF; break;
                case 'I': d->ido->q_indel = atoi(optarg); break;
                case 'G': d->ido->r_indel = atof(optarg); break;
+               case 'q': d->min_mapQ = atoi(optarg); break;
                default: fprintf(stderr, "Unrecognizd option '-%c'.\n", c); return 1;
                }
        }
@@ -306,6 +307,7 @@ int bam_pileup(int argc, char *argv[])
                fprintf(stderr, "Option: -s        simple (yet incomplete) pileup format\n");
                fprintf(stderr, "        -i        only show lines/consensus with indels\n");
                fprintf(stderr, "        -m INT    filtering reads with bits in INT [%d]\n", d->mask);
+               fprintf(stderr, "        -q INT    filtering reads with mapping quality smaller than INT [%d]\n", d->min_mapQ);
                fprintf(stderr, "        -M INT    cap mapping quality at INT [%d]\n", d->c->cap_mapQ);
                fprintf(stderr, "        -t FILE   list of reference sequences (assume the input is in SAM)\n");
                fprintf(stderr, "        -l FILE   list of sites at which pileup is output\n");
@@ -342,7 +344,7 @@ int bam_pileup(int argc, char *argv[])
                }
                d->h = fp->header;
                if (fn_pos) d->hash = load_pos(fn_pos, d->h);
-               sampileup(fp, d->mask, pileup_func, d);
+               sampileup(fp, d->mask, d->min_mapQ, pileup_func, d);
                samclose(fp); // d->h will be destroyed here
        }
 

diff --git a/bamtk.c b/bamtk.c
index 0fb7cb4c80494db3588a19e5f3ffd63005ccc9d9..844108220231f0f1a78fadd174e69d850959d898 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.4-2 (r316)"
+#define PACKAGE_VERSION "0.1.4-3 (r324)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);

diff --git a/sam.c b/sam.c
index 48a4b34ef10ee92280d5843a3ccd81593cd34540..9a6e201d75e24d366903ff4e937f80d71e45303c 100644 (file)
--- a/sam.c
+++ b/sam.c
@@ -116,7 +116,7 @@ int samwrite(samfile_t *fp, const bam1_t *b)
        }
 }
 
-int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data)
+int sampileup(samfile_t *fp, int mask, int min_mapQ, bam_pileup_f func, void *func_data)
 {
        bam_plbuf_t *buf;
        int ret;
@@ -125,7 +125,8 @@ int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data)
        buf = bam_plbuf_init(func, func_data);
        bam_plbuf_set_mask(buf, mask);
        while ((ret = samread(fp, b)) >= 0)
-               bam_plbuf_push(b, buf);
+               if (b->core.qual >= min_mapQ)
+                       bam_plbuf_push(b, buf);
        bam_plbuf_push(0, buf);
        bam_plbuf_destroy(buf);
        bam_destroy1(b);

diff --git a/sam.h b/sam.h
index 93daea6834d6f6b1c6fa6874ba52219045b671a2..082fe96b24913a2172b9b5b89036cb8fd91f1f0f 100644 (file)
--- a/sam.h
+++ b/sam.h
@@ -22,7 +22,7 @@ extern "C" {
        void samclose(samfile_t *fp);
        int samread(samfile_t *fp, bam1_t *b);
        int samwrite(samfile_t *fp, const bam1_t *b);
-       int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data);
+       int sampileup(samfile_t *fp, int mask, int min_mapQ, bam_pileup_f func, void *func_data);
 
 #ifdef __cplusplus
 }