Imported Upstream version 0.1.10

[samtools.git] / sam_view.c

diff --git a/sam_view.c b/sam_view.c
index d0fdad25445508e90052970a90de92e1f0f61ae5..eb69449f9e44d643ef43f31638fd8534c454c940 100644 (file)
--- a/sam_view.c
+++ b/sam_view.c
@@ -9,6 +9,13 @@
 #include "khash.h"
 KHASH_SET_INIT_STR(rg)
 
+// When counting records instead of printing them,
+// data passed to the bam_fetch callback is encapsulated in this struct.
+typedef struct {
+       bam_header_t *header;
+       int *count;
+} count_func_data_t;
+
 typedef khash_t(rg) *rghash_t;
 
 rghash_t g_rghash = 0;
@@ -54,7 +61,7 @@ static inline int __g_skip_aln(const bam_header_t *h, const bam1_t *b)
        return 0;
 }
 
-// callback function for bam_fetch()
+// callback function for bam_fetch() that prints nonskipped records
 static int view_func(const bam1_t *b, void *data)
 {
        if (!__g_skip_aln(((samfile_t*)data)->header, b))
@@ -62,19 +69,30 @@ static int view_func(const bam1_t *b, void *data)
        return 0;
 }
 
+// callback function for bam_fetch() that counts nonskipped records
+static int count_func(const bam1_t *b, void *data)
+{
+       if (!__g_skip_aln(((count_func_data_t*)data)->header, b)) {
+               (*((count_func_data_t*)data)->count)++;
+       }
+       return 0;
+}
+
 static int usage(int is_long_help);
 
 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 c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, is_uncompressed = 0, is_bamout = 0, slx2sngr = 0, is_count = 0;
        int of_type = BAM_OFDEC, is_long_help = 0;
+       int count = 0;
        samfile_t *in = 0, *out = 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:CR:")) >= 0) {
+       while ((c = getopt(argc, argv, "Sbct:hHo:q:f:F:ul:r:xX?T:CR:")) >= 0) {
                switch (c) {
+               case 'c': is_count = 1; break;
                case 'C': slx2sngr = 1; break;
                case 'S': is_bamin = 0; break;
                case 'b': is_bamout = 1; break;
@@ -133,7 +151,7 @@ int main_samview(int argc, char *argv[])
                ret = 1;
                goto view_end;
        }
-       if ((out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
+       if (!is_count && (out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
                fprintf(stderr, "[main_samview] fail to open \"%s\" for writing.\n", fn_out? fn_out : "standard output");
                ret = 1;
                goto view_end;
@@ -146,7 +164,8 @@ int main_samview(int argc, char *argv[])
                while ((r = samread(in, b)) >= 0) { // read one alignment from `in'
                        if (!__g_skip_aln(in->header, b)) {
                                if (slx2sngr) sol2sanger(b);
-                               samwrite(out, b); // write the alignment to `out'
+                               if (!is_count) samwrite(out, b); // write the alignment to `out'
+                               count++;
                        }
                }
                if (r < -1) {
@@ -164,14 +183,19 @@ int main_samview(int argc, char *argv[])
                        goto view_end;
                }
                for (i = optind + 1; i < argc; ++i) {
-                       int tid, beg, end;
+                       int tid, beg, end, result;
                        bam_parse_region(in->header, argv[i], &tid, &beg, &end); // parse a region in the format like `chr2:100-200'
                        if (tid < 0) { // reference name is not found
                                fprintf(stderr, "[main_samview] region \"%s\" specifies an unknown reference name. Continue anyway.\n", argv[i]);
                                continue;
                        }
                        // fetch alignments
-                       if (bam_fetch(in->x.bam, idx, tid, beg, end, out, view_func) < 0) {
+                       if (is_count) {
+                               count_func_data_t count_data = { in->header, &count };
+                               result = bam_fetch(in->x.bam, idx, tid, beg, end, &count_data, count_func);
+                       } else
+                               result = bam_fetch(in->x.bam, idx, tid, beg, end, out, view_func);
+                       if (result < 0) {
                                fprintf(stderr, "[main_samview] retrieval of region \"%s\" failed due to truncated file or corrupt BAM index file\n", argv[i]);
                                ret = 1;
                                break;
@@ -181,6 +205,9 @@ int main_samview(int argc, char *argv[])
        }
 
 view_end:
+       if (is_count && ret == 0) {
+               printf("%d\n", count);
+       }
        // close files, free and return
        free(fn_list); free(fn_ref); free(fn_out); free(g_library); free(g_rg); free(fn_rg);
        if (g_rghash) {
@@ -190,7 +217,8 @@ view_end:
                kh_destroy(rg, g_rghash);
        }
        samclose(in);
-       samclose(out);
+       if (!is_count)
+               samclose(out);
        return ret;
 }
 
@@ -205,6 +233,7 @@ static int usage(int is_long_help)
        fprintf(stderr, "         -u       uncompressed BAM output (force -b)\n");
        fprintf(stderr, "         -x       output FLAG in HEX (samtools-C specific)\n");
        fprintf(stderr, "         -X       output FLAG in string (samtools-C specific)\n");
+       fprintf(stderr, "         -c       print only the count of matching records\n");
        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");