* samtools-0.1.8-14 (r727)

 * allow to change the capQ parameter at the command line

diff --git a/bam_md.c b/bam_md.c
index eee767e08fb290ab1ea8baae778201e797c923c3..d2c84dcccd084c3399bf94ac6085af8902eb8532 100644 (file)
--- a/bam_md.c
+++ b/bam_md.c
@@ -110,14 +110,14 @@ void bam_fillmd1(bam1_t *b, char *ref, int is_equal)
        bam_fillmd1_core(b, ref, is_equal, 0);
 }
 
-int bam_cap_mapQ(bam1_t *b, char *ref)
+int bam_cap_mapQ(bam1_t *b, char *ref, int thres)
 {
        uint8_t *seq = bam1_seq(b), *qual = bam1_qual(b);
        uint32_t *cigar = bam1_cigar(b);
        bam1_core_t *c = &b->core;
        int i, x, y, mm, q, len, clip_l, clip_q;
        double t;
-
+       if (thres < 0) thres = 40; // set the default
        mm = q = len = clip_l = clip_q = 0;
        for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) {
                int j, l = cigar[i]>>4, op = cigar[i]&0xf;
@@ -154,10 +154,10 @@ int bam_cap_mapQ(bam1_t *b, char *ref)
        for (i = 0, t = 1; i < mm; ++i)
                t *= (double)len / (i+1);
        t = q - 4.343 * log(t) + clip_q / 5.;
-       if (t > 40) return -1;
+       if (t > thres) return -1;
        if (t < 0) t = 0;
-       t = sqrt((40 - t) / 40) * 40;
-       fprintf(stderr, "%s %lf %d\n", bam1_qname(b), t, q);
+       t = sqrt((thres - t) / thres) * thres;
+//     fprintf(stderr, "%s %lf %d\n", bam1_qname(b), t, q);
        return (int)(t + .499);
 }
 
@@ -320,7 +320,7 @@ int bam_fillmd(int argc, char *argv[])
                        }
                        if (is_realn) bam_realn(b, ref);
                        if (is_capQ) {
-                               int q = bam_cap_mapQ(b, ref);
+                               int q = bam_cap_mapQ(b, ref, 40);
                                if (b->core.qual > q) b->core.qual = q;
                        }
                        if (ref) bam_fillmd1_core(b, ref, is_equal, max_nm);

diff --git a/bam_plcmd.c b/bam_plcmd.c
index e9b3507ba74df7a471c78ca6670f44aa4c3f167a..20c5632b80d7c6a5c6c333ca2760af5a6f5dab6b 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -458,10 +458,9 @@ int bam_pileup(int argc, char *argv[])
 #define MPLP_NO_COMP 0x20
 #define MPLP_NO_ORPHAN 0x40
 #define MPLP_REALN   0x80
-#define MPLP_CAPQ    0x100
 
 typedef struct {
-       int max_mq, min_mq, flag, min_baseQ;
+       int max_mq, min_mq, flag, min_baseQ, capQ_thres;
        double theta;
        char *reg, *fn_pos;
        faidx_t *fai;
@@ -471,7 +470,7 @@ typedef struct {
 typedef struct {
        bamFile fp;
        bam_iter_t iter;
-       int min_mq, flag, ref_id;
+       int min_mq, flag, ref_id, capQ_thres;
        char *ref;
 } mplp_aux_t;
 
@@ -484,7 +483,7 @@ typedef struct {
 static int mplp_func(void *data, bam1_t *b)
 {
        extern int bam_realn(bam1_t *b, const char *ref);
-       extern int bam_cap_mapQ(bam1_t *b, char *ref);
+       extern int bam_cap_mapQ(bam1_t *b, char *ref, int thres);
        mplp_aux_t *ma = (mplp_aux_t*)data;
        int ret, skip = 0;
        do {
@@ -493,8 +492,8 @@ static int mplp_func(void *data, bam1_t *b)
                if (ret < 0) break;
                skip = 0;
                if (has_ref && (ma->flag&MPLP_REALN)) bam_realn(b, ma->ref);
-               if ((ma->flag&MPLP_CAPQ) && has_ref) {
-                       int q = bam_cap_mapQ(b, ma->ref);
+               if (has_ref && ma->capQ_thres > 10) {
+                       int q = bam_cap_mapQ(b, ma->ref, ma->capQ_thres);
                        if (q < 0) skip = 1;
                        else if (b->core.qual > q) b->core.qual = q;
                } else if (b->core.flag&BAM_FUNMAP) skip = 1;
@@ -561,6 +560,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                data[i] = calloc(1, sizeof(mplp_aux_t));
                data[i]->min_mq = conf->min_mq;
                data[i]->flag = conf->flag;
+               data[i]->capQ_thres = conf->capQ_thres;
                data[i]->fp = bam_open(fn[i], "r");
                h_tmp = bam_header_read(data[i]->fp);
                bam_smpl_add(sm, fn[i], h_tmp->text);
@@ -699,7 +699,8 @@ int bam_mpileup(int argc, char *argv[])
        mplp.max_mq = 60;
        mplp.theta = 1e-3;
        mplp.min_baseQ = 13;
-       while ((c = getopt(argc, argv, "gf:r:l:M:q:t:Q:uaORC")) >= 0) {
+       mplp.capQ_thres = 0;
+       while ((c = getopt(argc, argv, "gf:r:l:M:q:t:Q:uaORC:")) >= 0) {
                switch (c) {
                case 't': mplp.theta = atof(optarg); break;
                case 'f':
@@ -712,8 +713,8 @@ int bam_mpileup(int argc, char *argv[])
                case 'u': mplp.flag |= MPLP_NO_COMP; break;
                case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN; break;
                case 'O': mplp.flag |= MPLP_NO_ORPHAN; break;
-               case 'C': mplp.flag |= MPLP_CAPQ; break;
                case 'R': mplp.flag |= MPLP_REALN; 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;
                case 'Q': mplp.min_baseQ = atoi(optarg); break;

diff --git a/bamtk.c b/bamtk.c
index ce4ebd5f3aee472e0a12b2cae58da9aef5bf7e29..0ee62bc448b97661cd8a171fb089493aaeab8380 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.8-13 (r715)"
+#define PACKAGE_VERSION "0.1.8-14 (r727)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);