Adding -f flag to samtools sort to give output name directly.

diff --git a/bam_sort.c b/bam_sort.c
index 7d00cd1a83321729c1384cf56f066d2c83f65548..c46bce3b3f4ab2fbc5e5166b4bfaf2ff12b013a9 100644 (file)
--- a/bam_sort.c
+++ b/bam_sort.c
@@ -434,12 +434,13 @@ static int sort_blocks(int n_files, size_t k, bam1_p *buf, const char *prefix, c
   @param  prefix   prefix of the output and the temporary files; upon
                           sucessess, prefix.bam will be written.
   @param  max_mem  approxiate maximum memory (very inaccurate)
+  @param full_path the given output path is the full path and not just the prefix
 
   @discussion It may create multiple temporary subalignment files
   and then merge them by calling bam_merge_core(). This function is
   NOT thread safe.
  */
-void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size_t _max_mem, int is_stdout, int n_threads, int level)
+void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size_t _max_mem, int is_stdout, int n_threads, int level, int full_path)
 {
        int ret, i, n_files = 0;
        size_t mem, max_k, k, max_mem;
@@ -447,6 +448,8 @@ void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size
        bamFile fp;
        bam1_t *b, **buf;
        char *fnout = 0;
+       char const *suffix = ".bam";
+       if (full_path) suffix += 4;
 
        if (n_threads < 2) n_threads = 1;
        g_is_by_qname = is_by_qname;
@@ -489,7 +492,7 @@ void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size
        // output file name
        fnout = calloc(strlen(prefix) + 20, 1);
        if (is_stdout) sprintf(fnout, "-");
-       else sprintf(fnout, "%s.bam", prefix);
+       else sprintf(fnout, "%s%s", prefix, suffix);
        // write the final output
        if (n_files == 0) { // a single block
                char mode[8];
@@ -504,7 +507,7 @@ void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size
                fns = (char**)calloc(n_files, sizeof(char*));
                for (i = 0; i < n_files; ++i) {
                        fns[i] = (char*)calloc(strlen(prefix) + 20, 1);
-                       sprintf(fns[i], "%s.%.4d.bam", prefix, i);
+                       sprintf(fns[i], "%s.%.4d%s", prefix, i, suffix);
                }
                bam_merge_core2(is_by_qname, fnout, 0, n_files, fns, 0, 0, n_threads, level);
                for (i = 0; i < n_files; ++i) {
@@ -527,15 +530,16 @@ void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size
 
 void bam_sort_core(int is_by_qname, const char *fn, const char *prefix, size_t max_mem)
 {
-       bam_sort_core_ext(is_by_qname, fn, prefix, max_mem, 0, 0, -1);
+       bam_sort_core_ext(is_by_qname, fn, prefix, max_mem, 0, 0, -1, 0);
 }
 
 int bam_sort(int argc, char *argv[])
 {
        size_t max_mem = 768<<20; // 512MB
-       int c, is_by_qname = 0, is_stdout = 0, n_threads = 0, level = -1;
-       while ((c = getopt(argc, argv, "nom:@:l:")) >= 0) {
+       int c, is_by_qname = 0, is_stdout = 0, n_threads = 0, level = -1, full_path = 0;
+       while ((c = getopt(argc, argv, "fnom:@:l:")) >= 0) {
                switch (c) {
+               case 'f': full_path = 1; break;
                case 'o': is_stdout = 1; break;
                case 'n': is_by_qname = 1; break;
                case 'm': {
@@ -554,6 +558,7 @@ int bam_sort(int argc, char *argv[])
                fprintf(stderr, "\n");
                fprintf(stderr, "Usage:   samtools sort [options] <in.bam> <out.prefix>\n\n");
                fprintf(stderr, "Options: -n        sort by read name\n");
+               fprintf(stderr, "         -f        use <out.prefix> as full file name instead of prefix\n");
                fprintf(stderr, "         -o        final output to stdout\n");
                fprintf(stderr, "         -l INT    compression level, from 0 to 9 [-1]\n");
                fprintf(stderr, "         -@ INT    number of sorting and compression threads [1]\n");
@@ -561,6 +566,6 @@ int bam_sort(int argc, char *argv[])
                fprintf(stderr, "\n");
                return 1;
        }
-       bam_sort_core_ext(is_by_qname, argv[optind], argv[optind+1], max_mem, is_stdout, n_threads, level);
+       bam_sort_core_ext(is_by_qname, argv[optind], argv[optind+1], max_mem, is_stdout, n_threads, level, full_path);
        return 0;
 }

diff --git a/samtools.1 b/samtools.1
index 718ac392016705cb758d4cded7eeded2755faff2..118a6e83079bddd9787e89673d64e7a4b1ddd0b3 100644 (file)
--- a/samtools.1
+++ b/samtools.1
@@ -328,7 +328,7 @@ which enables fast BAM concatenation.
 
 .TP
 .B sort
-samtools sort [-no] [-m maxMem] <in.bam> <out.prefix>
+samtools sort [-nof] [-m maxMem] <in.bam> <out.prefix>
 
 Sort alignments by leftmost coordinates. File
 .I <out.prefix>.bam
@@ -346,6 +346,13 @@ Output the final alignment to the standard output.
 .B -n
 Sort by read names rather than by chromosomal coordinates
 .TP
+.B -f
+Use
+.I <out.prefix>
+as the full output path and do not append
+.I .bam
+suffix.
+.TP
 .BI -m \ INT
 Approximately the maximum required memory. [500000000]
 .RE