* samtools-0.1.12-10 (r896)

 * allow to exclude read groups in mpileup

diff --git a/bam_plcmd.c b/bam_plcmd.c
index d03bab10af0efe28cbda757b3c7e1a7150bfde1d..d6e8213e51c2d9938d15ced14b4eee0ff3859610 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -542,13 +542,15 @@ typedef struct {
        char *reg, *fn_pos, *pl_list;
        faidx_t *fai;
        kh_64_t *hash;
+       void *rghash;
 } mplp_conf_t;
 
 typedef struct {
        bamFile fp;
        bam_iter_t iter;
-       int min_mq, flag, ref_id, capQ_thres;
+       int ref_id;
        char *ref;
+       const mplp_conf_t *conf;
 } mplp_aux_t;
 
 typedef struct {
@@ -568,16 +570,21 @@ static int mplp_func(void *data, bam1_t *b)
                int has_ref;
                ret = ma->iter? bam_iter_read(ma->fp, ma->iter, b) : bam_read1(ma->fp, b);
                if (ret < 0) break;
+               if (ma->conf->rghash) { // exclude read groups
+                       uint8_t *rg = bam_aux_get(b, "RG");
+                       skip = (rg && bcf_str2id(ma->conf->rghash, (const char*)(rg+1)) >= 0);
+                       if (skip) continue;
+               }
                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, (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 (has_ref && (ma->conf->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, (ma->conf->flag & MPLP_EXT_BAQ)? 3 : 1);
+               if (has_ref && ma->conf->capQ_thres > 10) {
+                       int q = bam_cap_mapQ(b, ma->ref, ma->conf->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;
-               else if (b->core.qual < ma->min_mq) skip = 1; 
-               else if ((ma->flag&MPLP_NO_ORPHAN) && (b->core.flag&1) && !(b->core.flag&2)) skip = 1;
+               else if (b->core.qual < ma->conf->min_mq) skip = 1; 
+               else if ((ma->conf->flag&MPLP_NO_ORPHAN) && (b->core.flag&1) && !(b->core.flag&2)) skip = 1;
        } while (skip);
        return ret;
 }
@@ -640,10 +647,8 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
        for (i = 0; i < n; ++i) {
                bam_header_t *h_tmp;
                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 = strcmp(fn[i], "-") == 0? bam_dopen(fileno(stdin), "r") : bam_open(fn[i], "r");
+               data[i]->conf = conf;
                h_tmp = bam_header_read(data[i]->fp);
                bam_smpl_add(sm, fn[i], h_tmp->text);
                rghash = bcf_call_add_rg(rghash, h_tmp->text, conf->pl_list);
@@ -801,7 +806,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 }
 
 #define MAX_PATH_LEN 1024
-int read_file_list(const char *file_list,int *n,char **argv[])
+static int read_file_list(const char *file_list,int *n,char **argv[])
 {
     char buf[MAX_PATH_LEN];
     int len, nfiles;
@@ -864,7 +869,7 @@ 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:b:P:o:e:h:Im:F:E")) >= 0) {
+       while ((c = getopt(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:b:P:o:e:h:Im:F:EG:")) >= 0) {
                switch (c) {
                case 'f':
                        mplp.fai = fai_load(optarg);
@@ -894,6 +899,17 @@ int bam_mpileup(int argc, char *argv[])
                case 'A': use_orphan = 1; break;
                case 'F': mplp.min_frac = atof(optarg); break;
                case 'm': mplp.min_support = atoi(optarg); break;
+               case 'G': {
+                               FILE *fp_rg;
+                               char buf[1024];
+                               mplp.rghash = bcf_str2id_init();
+                               if ((fp_rg = fopen(optarg, "r")) == 0)
+                                       fprintf(stderr, "(%s) Fail to open file %s. Continue anyway.\n", __func__, optarg);
+                               while (!feof(fp_rg) && fscanf(fp_rg, "%s", buf) > 0) // this is not a good style, but forgive me...
+                                       bcf_str2id_add(mplp.rghash, strdup(buf));
+                               fclose(fp_rg);
+                       }
+                       break;
                }
        }
        if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN;
@@ -914,6 +930,7 @@ int bam_mpileup(int argc, char *argv[])
                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, "         -G FILE     exclude read groups listed in FILE [null]\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");
@@ -925,15 +942,13 @@ int bam_mpileup(int argc, char *argv[])
                fprintf(stderr, "Notes: Assuming diploid individuals.\n\n");
                return 1;
        }
-    if ( file_list )
-    {
+    if (file_list) {
         if ( read_file_list(file_list,&nfiles,&fn) ) return 1;
         mpileup(&mplp,nfiles,fn);
         for (c=0; c<nfiles; c++) free(fn[c]);
         free(fn);
-    }
-    else
-           mpileup(&mplp, argc - optind, argv + optind);
+    } else mpileup(&mplp, argc - optind, argv + optind);
+       if (mplp.rghash) bcf_str2id_thorough_destroy(mplp.rghash);
        free(mplp.reg); free(mplp.pl_list);
        if (mplp.fai) fai_destroy(mplp.fai);
        return 0;

diff --git a/bamtk.c b/bamtk.c
index 576ff7dbeab9309b0ede73d37ca2d2f77e269d65..f2b577cca629a9a761045337828b460282f437bf 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.12-9 (r891)"
+#define PACKAGE_VERSION "0.1.12-10 (r896)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);

diff --git a/bcftools/bcf.h b/bcftools/bcf.h
index 84f0c2d941eb24db6a8c3b0cbc015e2402d80a1e..6932f35147a72c88fb7a4bd9bed682403c677a4c 100644 (file)
--- a/bcftools/bcf.h
+++ b/bcftools/bcf.h
@@ -148,6 +148,7 @@ extern "C" {
        // string hash table
        void *bcf_build_refhash(bcf_hdr_t *h);
        void bcf_str2id_destroy(void *_hash);
+       void bcf_str2id_thorough_destroy(void *_hash);
        int bcf_str2id_add(void *_hash, const char *str);
        int bcf_str2id(void *_hash, const char *str);
        void *bcf_str2id_init();

diff --git a/bcftools/bcfutils.c b/bcftools/bcfutils.c
index fb70d81ae8c1c50d765176860c55719388f5b260..8a8e0c98a94dbbfbdd856f5c36375eb5ffc0e345 100644 (file)
--- a/bcftools/bcfutils.c
+++ b/bcftools/bcfutils.c
@@ -29,6 +29,16 @@ void bcf_str2id_destroy(void *_hash)
        if (hash) kh_destroy(str2id, hash); // Note that strings are not freed.
 }
 
+void bcf_str2id_thorough_destroy(void *_hash)
+{
+       khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
+       khint_t k;
+       if (hash == 0) return;
+       for (k = 0; k < kh_end(hash); ++k)
+               if (kh_exist(hash, k)) free((char*)kh_key(hash, k));
+       kh_destroy(str2id, hash);
+}
+
 int bcf_str2id(void *_hash, const char *str)
 {
        khash_t(str2id) *hash = (khash_t(str2id)*)_hash;

diff --git a/bcftools/call1.c b/bcftools/call1.c
index 809fe344bfd0a7abf822b82db3670c25ed47689c..e4ba879a64b3d6bdd4f9ff230457b6e4394c784b 100644 (file)
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -208,8 +208,10 @@ static char **read_samples(const char *fn, int *_n)
        kstring_t s;
        int dret, n = 0, max = 0;
        char **sam = 0;
+       *_n = 0;
        s.l = s.m = 0; s.s = 0;
        fp = gzopen(fn, "r");
+       if (fp == 0) return 0; // fail to open file
        ks = ks_init(fp);
        while (ks_getuntil(ks, 0, &s, &dret) >= 0) {
                if (max == n) {