* samtools-0.1.8-12 (r692)

 * group data by samples in "mpileup -g"

diff --git a/Makefile b/Makefile
index 6a15c284a90eae0632e9dfbc86c89ba08c7bb16b..3ff3272165c5e87e1bcda15bcade2baf100b53ad 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -7,7 +7,7 @@ LOBJS=          bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
                        $(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o
 AOBJS=         bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o \
                        bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o     \
-                       bamtk.o kaln.o bam2bcf.o errmod.o
+                       bamtk.o kaln.o bam2bcf.o errmod.o sample.o
 PROG=          samtools
 INCLUDES=      -I.
 SUBDIRS=       . bcftools misc

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 80799e3b28af95208796424c31a4bf5b7dd24ba0..a23477f40ec3147db38529140b09bac5531af54b 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -5,7 +5,6 @@
 #include "sam.h"
 #include "faidx.h"
 #include "bam_maqcns.h"
-#include "bam2bcf.h"
 #include "khash.h"
 #include "glf.h"
 #include "kstring.h"
@@ -449,6 +448,10 @@ int bam_pileup(int argc, char *argv[])
  * mpileup *
  ***********/
 
+#include <assert.h>
+#include "bam2bcf.h"
+#include "sample.h"
+
 #define MPLP_GLF   0x10
 #define MPLP_NO_COMP 0x20
 
@@ -466,6 +469,12 @@ typedef struct {
        int min_mq;
 } mplp_aux_t;
 
+typedef struct {
+       int n;
+       int *n_plp, *m_plp;
+       bam_pileup1_t **plp;
+} mplp_pileup_t;
+
 static int mplp_func(void *data, bam1_t *b)
 {
        mplp_aux_t *ma = (mplp_aux_t*)data;
@@ -476,6 +485,29 @@ static int mplp_func(void *data, bam1_t *b)
        return ret;
 }
 
+static void group_smpl(mplp_pileup_t *m, bam_sample_t *sm, kstring_t *buf,
+                                          int n, char *const*fn, int *n_plp, const bam_pileup1_t **plp)
+{
+       int i, j;
+       memset(m->n_plp, 0, m->n * sizeof(int));
+       for (i = 0; i < n; ++i) {
+               for (j = 0; j < n_plp[i]; ++j) {
+                       const bam_pileup1_t *p = plp[i] + j;
+                       uint8_t *q;
+                       int id = -1;
+                       q = bam_aux_get(p->b, "RG");
+                       if (q) id = bam_smpl_rg2smid(sm, fn[i], (char*)q+1, buf);
+                       if (id < 0) id = bam_smpl_rg2smid(sm, fn[i], 0, buf);
+                       assert(id >= 0 && id < m->n);
+                       if (m->n_plp[id] == m->m_plp[id]) {
+                               m->m_plp[id] = m->m_plp[id]? m->m_plp[id]<<1 : 8;
+                               m->plp[id] = realloc(m->plp[id], sizeof(bam_pileup1_t) * m->m_plp[id]);
+                       }
+                       m->plp[id][m->n_plp[id]++] = *p;
+               }
+       }
+}
+
 static int mpileup(mplp_conf_t *conf, int n, char **fn)
 {
        mplp_aux_t **data;
@@ -492,10 +524,17 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
        bcf_t *bp = 0;
        bcf_hdr_t *bh = 0;
 
+       bam_sample_t *sm = 0;
+       kstring_t buf;
+       mplp_pileup_t gplp;
+
+       memset(&gplp, 0, sizeof(mplp_pileup_t));
+       memset(&buf, 0, sizeof(kstring_t));
        memset(&bc, 0, sizeof(bcf_call_t));
        data = calloc(n, sizeof(void*));
        plp = calloc(n, sizeof(void*));
        n_plp = calloc(n, sizeof(int*));
+       sm = bam_smpl_init();
 
        // read the header and initialize data
        for (i = 0; i < n; ++i) {
@@ -504,6 +543,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                data[i]->min_mq = conf->min_mq;
                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);
                if (conf->reg) {
                        int beg, end;
                        bam_index_t *idx;
@@ -526,6 +566,12 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                        bam_header_destroy(h_tmp);
                }
        }
+       gplp.n = sm->n;
+       gplp.n_plp = calloc(sm->n, sizeof(int));
+       gplp.m_plp = calloc(sm->n, sizeof(int));
+       gplp.plp = calloc(sm->n, sizeof(void*));
+
+       fprintf(stderr, "[%s] %d samples in %d input files\n", __func__, sm->n, n);
        if (conf->fn_pos) hash = load_pos(conf->fn_pos, h);
        // write the VCF header
        if (conf->flag & MPLP_GLF) {
@@ -541,12 +587,8 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                bh->name = malloc(s.l);
                memcpy(bh->name, s.s, s.l);
                s.l = 0;
-               for (i = 0; i < n; ++i) {
-                       const char *p;
-                       if ((p = strstr(fn[i], ".bam")) != 0)
-                               kputsn(fn[i], p - fn[i], &s);
-                       else kputs(fn[i], &s);
-                       kputc('\0', &s);
+               for (i = 0; i < sm->n; ++i) {
+                       kputs(sm->smpl[i], &s); kputc('\0', &s);
                }
                bh->l_smpl = s.l;
                bh->sname = malloc(s.l);
@@ -555,11 +597,8 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                free(s.s);
                bcf_hdr_sync(bh);
                bcf_hdr_write(bp, bh);
-       }
-       // mpileup
-       if (conf->flag & MPLP_GLF) {
                bca = bcf_call_init(-1., conf->min_baseQ);
-               bcr = calloc(n, sizeof(bcf_callret1_t));
+               bcr = calloc(sm->n, sizeof(bcf_callret1_t));
        }
        ref_tid = -1; ref = 0;
        iter = bam_mplp_init(n, mplp_func, (void**)data);
@@ -578,14 +617,14 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                if (conf->flag & MPLP_GLF) {
                        int _ref0, ref16;
                        bcf1_t *b = calloc(1, sizeof(bcf1_t));
+                       group_smpl(&gplp, sm, &buf, n, fn, n_plp, plp);
                        _ref0 = (ref && pos < ref_len)? ref[pos] : 'N';
                        ref16 = bam_nt16_table[_ref0];
-                       for (i = 0; i < n; ++i)
-                               bcf_call_glfgen(n_plp[i], plp[i], ref16, bca, bcr + i);
-                       bcf_call_combine(n, bcr, ref16, &bc);
+                       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_write(bp, bh, b);
-                       //fprintf(stderr, "%d,%d,%d\n", b->tid, b->pos, b->l_str);
                        bcf_destroy(b);
                } else {
                        printf("%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N');
@@ -608,7 +647,11 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                        putchar('\n');
                }
        }
+
        bcf_close(bp);
+       bam_smpl_destroy(sm); free(buf.s);
+       for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]);
+       free(gplp.plp); free(gplp.n_plp); free(gplp.m_plp);
        if (hash) { // free the hash table
                khint_t k;
                for (k = kh_begin(hash); k < kh_end(hash); ++k)

diff --git a/bamtk.c b/bamtk.c
index 480f7468a12d0342cf2acf746fb17f34929372a5..d4b40eab0166dd062e04438dff8b69cedb5a9328 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.8-11 (r672)"
+#define PACKAGE_VERSION "0.1.8-12 (r693)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);

diff --git a/examples/Makefile b/examples/Makefile
index 96a4e7ed96d14ebf38013ff60216d6cda25bfa49..2733a573ffbecc5a33599bb9e7425b7f9d3be994 100644 (file)
--- a/examples/Makefile
+++ b/examples/Makefile
@@ -19,7 +19,7 @@ ex1a.bam:ex1.bam
 ex1b.bam:ex1.bam
                ../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$$1=$$1"b";print}}' | ../samtools view -bS - > $@
 ex1f.rg:
-               (echo "@RG      ID:ex1  LB:ex1"; echo "@RG      ID:ex1a LB:ex1"; echo "@RG      ID:ex1b LB:ex1b") > $@
+               (echo "@RG      ID:ex1  LB:ex1  SM:ex1"; echo "@RG      ID:ex1a LB:ex1  SM:ex1"; echo "@RG      ID:ex1b LB:ex1b SM:ex1b") > $@
 ex1f.bam:ex1.bam ex1a.bam ex1b.bam ex1f.rg
                ../samtools merge -rh ex1f.rg $@ ex1.bam ex1a.bam ex1b.bam
 ex1f-rmduppe.bam:ex1f.bam

diff --git a/sample.c b/sample.c
new file mode 100644 (file)
index 0000000..95bec68
--- /dev/null
+++ b/sample.c
@@ -0,0 +1,92 @@
+#include <stdlib.h>
+#include <string.h>
+#include "sample.h"
+#include "khash.h"
+KHASH_MAP_INIT_STR(sm, int)
+
+bam_sample_t *bam_smpl_init(void)
+{
+       bam_sample_t *s;
+       s = calloc(1, sizeof(bam_sample_t));
+       s->rg2smid = kh_init(sm);
+       return s;
+}
+
+void bam_smpl_destroy(bam_sample_t *sm)
+{
+       int i;
+       khint_t k;
+       khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
+       if (sm == 0) return;
+       for (i = 0; i < sm->n; ++i) free(sm->smpl[i]);
+       free(sm->smpl);
+       for (k = kh_begin(rg2smid); k != kh_end(rg2smid); ++k)
+               if (kh_exist(rg2smid, k)) free((char*)kh_key(rg2smid, k));
+       kh_destroy(sm, sm->rg2smid);
+       free(sm);
+}
+
+static void add_pair(bam_sample_t *sm, khash_t(sm) *sm2id, const char *key, const char *val)
+{
+       khint_t k_rg, k_sm;
+       int ret;
+       khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
+       k_rg = kh_get(sm, rg2smid, key);
+       if (k_rg != kh_end(rg2smid)) return; // duplicated @RG-ID
+       k_rg = kh_put(sm, rg2smid, strdup(key), &ret);
+       k_sm = kh_get(sm, sm2id, val);
+       if (k_sm == kh_end(sm2id)) { // absent
+               if (sm->n == sm->m) {
+                       sm->m = sm->m? sm->m<<1 : 1;
+                       sm->smpl = realloc(sm->smpl, sizeof(void*) * sm->m);
+               }
+               sm->smpl[sm->n] = strdup(val);
+               k_sm = kh_put(sm, sm2id, sm->smpl[sm->n], &ret);
+               kh_val(sm2id, k_sm) = sm->n++;
+       }
+       kh_val(rg2smid, k_rg) = kh_val(sm2id, k_sm);
+}
+
+int bam_smpl_add(bam_sample_t *sm, const char *fn, const char *txt)
+{
+       const char *p = txt, *q, *r;
+       kstring_t buf;
+       int n = 0;
+       khash_t(sm) *sm2id;
+       sm2id = kh_init(sm);
+       memset(&buf, 0, sizeof(kstring_t));
+       while ((q = strstr(p, "@RG")) != 0) {
+               p = q + 3;
+               r = q = 0;
+               if ((q = strstr(p, "\tID:")) != 0) q += 4;
+               if ((r = strstr(p, "\tSM:")) != 0) r += 4;
+               if (r && q) {
+                       char *u, *v;
+                       int oq, or;
+                       for (u = (char*)q; *u && *u != '\t' && *u != '\n'; ++u);
+                       for (v = (char*)r; *v && *v != '\t' && *v != '\n'; ++v);
+                       oq = *u; or = *v; *u = *v = '\0';
+                       buf.l = 0; kputs(fn, &buf); kputc('/', &buf); kputs(q, &buf);
+                       add_pair(sm, sm2id, buf.s, r);
+                       *u = oq; *v = or;
+               } else break;
+               p = q > r? q : r;
+               ++n;
+       }
+       if (n == 0) add_pair(sm, sm2id, fn, fn);
+       free(buf.s);
+       kh_destroy(sm, sm2id);
+       return 0;
+}
+
+int bam_smpl_rg2smid(const bam_sample_t *sm, const char *fn, const char *rg, kstring_t *str)
+{
+       khint_t k;
+       khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
+       if (rg) {
+               str->l = 0;
+               kputs(fn, str); kputc('/', str); kputs(rg, str);
+               k = kh_get(sm, rg2smid, str->s);
+       } else k = kh_get(sm, rg2smid, fn);
+       return k == kh_end(rg2smid)? -1 : kh_val(rg2smid, k);
+}

diff --git a/sample.h b/sample.h
new file mode 100644 (file)
index 0000000..149f380
--- /dev/null
+++ b/sample.h
@@ -0,0 +1,17 @@
+#ifndef BAM_SAMPLE_H
+#define BAM_SAMPLE_H
+
+#include "kstring.h"
+
+typedef struct {
+       int n, m;
+       char **smpl;
+       void *rg2smid;
+} bam_sample_t;
+
+bam_sample_t *bam_smpl_init(void);
+int bam_smpl_add(bam_sample_t *sm, const char *abs, const char *txt);
+int bam_smpl_rg2smid(const bam_sample_t *sm, const char *fn, const char *rg, kstring_t *str);
+void bam_smpl_destroy(bam_sample_t *sm);
+
+#endif