Imported Upstream version 0.1.8

[samtools.git] / sam_view.c

diff --git a/sam_view.c b/sam_view.c
index 06dd01a5ffa951dcb950a97681e7c5aca0b88971..3b10e2e5372e98a2b9ebda4bd5791dc1b837a20f 100644 (file)
--- a/sam_view.c
+++ b/sam_view.c
@@ -6,7 +6,12 @@
 #include "sam_header.h"
 #include "sam.h"
 #include "faidx.h"
+#include "khash.h"
+KHASH_SET_INIT_STR(rg)
 
+typedef khash_t(rg) *rghash_t;
+
+rghash_t g_rghash = 0;
 static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0;
 static char *g_library, *g_rg;
 static int g_sol2sanger_tbl[128];
@@ -32,9 +37,15 @@ static inline int __g_skip_aln(const bam_header_t *h, const bam1_t *b)
 {
        if (b->core.qual < g_min_mapQ || ((b->core.flag & g_flag_on) != g_flag_on) || (b->core.flag & g_flag_off))
                return 1;
-       if (g_rg) {
+       if (g_rg || g_rghash) {
                uint8_t *s = bam_aux_get(b, "RG");
-               if (s && strcmp(g_rg, (char*)(s + 1)) == 0) return 0;
+               if (s) {
+                       if (g_rg) return (strcmp(g_rg, (char*)(s + 1)) == 0)? 0 : 1;
+                       if (g_rghash) {
+                               khint_t k = kh_get(rg, g_rghash, (char*)(s + 1));
+                               return (k != kh_end(g_rghash))? 0 : 1;
+                       }
+               }
        }
        if (g_library) {
                const char *p = bam_get_library((bam_header_t*)h, b);
@@ -58,11 +69,11 @@ int main_samview(int argc, char *argv[])
        int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, is_uncompressed = 0, is_bamout = 0, slx2sngr = 0;
        int of_type = BAM_OFDEC, is_long_help = 0;
        samfile_t *in = 0, *out = 0;
-       char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0;
+       char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0, *fn_rg = 0;
 
        /* parse command-line options */
        strcpy(in_mode, "r"); strcpy(out_mode, "w");
-       while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:ul:r:xX?T:C")) >= 0) {
+       while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:ul:r:xX?T:CR:")) >= 0) {
                switch (c) {
                case 'C': slx2sngr = 1; break;
                case 'S': is_bamin = 0; break;
@@ -77,6 +88,7 @@ int main_samview(int argc, char *argv[])
                case 'u': is_uncompressed = 1; break;
                case 'l': g_library = strdup(optarg); break;
                case 'r': g_rg = strdup(optarg); break;
+               case 'R': fn_rg = strdup(optarg); break;
                case 'x': of_type = BAM_OFHEX; break;
                case 'X': of_type = BAM_OFSTR; break;
                case '?': is_long_help = 1; break;
@@ -94,7 +106,19 @@ int main_samview(int argc, char *argv[])
        if (is_bamin) strcat(in_mode, "b");
        if (is_header) strcat(out_mode, "h");
        if (is_uncompressed) strcat(out_mode, "u");
-       if (argc == optind) return usage(is_long_help);
+       if (argc == optind) return usage(is_long_help); // potential memory leak...
+
+       // read the list of read groups
+       if (fn_rg) {
+               FILE *fp_rg;
+               char buf[1024];
+               int ret;
+               g_rghash = kh_init(rg);
+               fp_rg = fopen(fn_rg, "r");
+               while (!feof(fp_rg) && fscanf(fp_rg, "%s", buf) > 0) // this is not a good style, but bear me...
+                       kh_put(rg, g_rghash, strdup(buf), &ret); // we'd better check duplicates...
+               fclose(fp_rg);
+       }
 
        // generate the fn_list if necessary
        if (fn_list == 0 && fn_ref) fn_list = samfaipath(fn_ref);
@@ -147,7 +171,13 @@ int main_samview(int argc, char *argv[])
 
 view_end:
        // close files, free and return
-       free(fn_list); free(fn_ref); free(fn_out); free(g_library); free(g_rg);
+       free(fn_list); free(fn_ref); free(fn_out); free(g_library); free(g_rg); free(fn_rg);
+       if (g_rghash) {
+               khint_t k;
+               for (k = 0; k < kh_end(g_rghash); ++k)
+                       if (kh_exist(g_rghash, k)) free((char*)kh_key(g_rghash, k));
+               kh_destroy(rg, g_rghash);
+       }
        samclose(in);
        samclose(out);
        return ret;
@@ -167,6 +197,7 @@ static int usage(int is_long_help)
        fprintf(stderr, "         -t FILE  list of reference names and lengths (force -S) [null]\n");
        fprintf(stderr, "         -T FILE  reference sequence file (force -S) [null]\n");
        fprintf(stderr, "         -o FILE  output file name [stdout]\n");
+       fprintf(stderr, "         -R FILE  list of read groups to be outputted [null]\n");
        fprintf(stderr, "         -f INT   required flag, 0 for unset [0]\n");
        fprintf(stderr, "         -F INT   filtering flag, 0 for unset [0]\n");
        fprintf(stderr, "         -q INT   minimum mapping quality [0]\n");