* samtools-0.1.8-1 (r615)

 * allow to get mpileup at required sites

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 6804795bd107405982cada8544051cc073fdf55e..c665a923a8a2ec1eaab957444012689ffd8fab16 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -449,8 +449,9 @@ int bam_pileup(int argc, char *argv[])
  ***********/
 
 typedef struct {
-       char *reg;
+       char *reg, *fn_pos;
        faidx_t *fai;
+       kh_64_t *hash;
 } mplp_conf_t;
 
 typedef struct {
@@ -473,6 +474,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
        bam_mplp_t iter;
        bam_header_t *h = 0;
        char *ref;
+       khash_t(64) *hash = 0;
        // allocate
        data = calloc(n, sizeof(void*));
        plp = calloc(n, sizeof(void*));
@@ -505,11 +507,17 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                        bam_header_destroy(h_tmp);
                }
        }
+       if (conf->fn_pos) hash = load_pos(conf->fn_pos, h);
        // mpileup
        ref_tid = -1; ref = 0;
        iter = bam_mplp_init(n, mplp_func, (void**)data);
        while (bam_mplp_auto(iter, &tid, &pos, n_plp, plp) > 0) {
                if (conf->reg && (pos < beg0 || pos >= end0)) continue; // out of the region requested
+               if (hash) {
+                       khint_t k;
+                       k = kh_get(64, hash, (uint64_t)tid<<32 | pos);
+                       if (k == kh_end(hash)) continue;
+               }
                if (tid != ref_tid) {
                        free(ref);
                        if (conf->fai) ref = fai_fetch(conf->fai, h->target_name[tid], &ref_len);
@@ -534,6 +542,12 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                }
                putchar('\n');
        }
+       if (hash) { // free the hash table
+               khint_t k;
+               for (k = kh_begin(hash); k < kh_end(hash); ++k)
+                       if (kh_exist(hash, k)) free(kh_val(hash, k));
+               kh_destroy(64, hash);
+       }
        bam_mplp_destroy(iter);
        bam_header_destroy(h);
        for (i = 0; i < n; ++i) {
@@ -550,17 +564,18 @@ int bam_mpileup(int argc, char *argv[])
        int c;
        mplp_conf_t mplp;
        memset(&mplp, 0, sizeof(mplp_conf_t));
-       while ((c = getopt(argc, argv, "f:r:")) >= 0) {
+       while ((c = getopt(argc, argv, "f:r:l:")) >= 0) {
                switch (c) {
                case 'f':
                        mplp.fai = fai_load(optarg);
                        if (mplp.fai == 0) return 1;
                        break;
-               case 'r': mplp.reg = strdup(optarg);
+               case 'r': mplp.reg = strdup(optarg); break;
+               case 'l': mplp.fn_pos = strdup(optarg); break;
                }
        }
        if (argc == 1) {
-               fprintf(stderr, "Usage: samtools mpileup [-r reg] [-f in.fa] in1.bam [in2.bam [...]]\n");
+               fprintf(stderr, "Usage: samtools mpileup [-r reg] [-f in.fa] [-l pos] in1.bam [in2.bam [...]]\n");
                return 1;
        }
        mpileup(&mplp, argc - optind, argv + optind);

diff --git a/bamtk.c b/bamtk.c
index 94c4d3fdb34be8698e21e9cf20166cadd1ae06c8..f93cf524c3ef8ec6eda5e76d2929802801437f9e 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.8 (r613)"
+#define PACKAGE_VERSION "0.1.8-1 (r615)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);

diff --git a/misc/Makefile b/misc/Makefile
index 2d7139d4e8a5c62068afb381f47493f8408bc681..6c25c782eb4e2ad784563991bd69922e885737cb 100644 (file)
--- a/misc/Makefile
+++ b/misc/Makefile
@@ -1,6 +1,6 @@
 CC=                    gcc
 CXX=           g++
-CFLAGS=                -g -Wall #-O2 #-m64 #-arch ppc
+CFLAGS=                -g -Wall -O2 #-m64 #-arch ppc
 CXXFLAGS=      $(CFLAGS)
 DFLAGS=                -D_FILE_OFFSET_BITS=64
 OBJS=