Updated samtools to 0.1.19

[rsem.git] / sam / bamshuf.c

diff --git a/sam/bamshuf.c b/sam/bamshuf.c
new file mode 100644 (file)
index 0000000..33a5238
--- /dev/null
+++ b/sam/bamshuf.c
@@ -0,0 +1,141 @@
+#include <unistd.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <assert.h>
+#include "sam.h"
+#include "ksort.h"
+
+#define DEF_CLEVEL 1
+
+static inline unsigned hash_Wang(unsigned key)
+{
+    key += ~(key << 15);
+    key ^=  (key >> 10);
+    key +=  (key << 3);
+    key ^=  (key >> 6);
+    key += ~(key << 11);
+    key ^=  (key >> 16);
+    return key;
+}
+
+static inline unsigned hash_X31_Wang(const char *s)
+{
+       unsigned h = *s;
+       if (h) {
+               for (++s ; *s; ++s) h = (h << 5) - h + *s;
+               return hash_Wang(h);
+       } else return 0;
+}
+
+typedef struct {
+       unsigned key;
+       bam1_t *b;
+} elem_t;
+
+static inline int elem_lt(elem_t x, elem_t y)
+{
+       if (x.key < y.key) return 1;
+       if (x.key == y.key) {
+               int t;
+               t = strcmp(bam_get_qname(x.b), bam_get_qname(y.b));
+               if (t < 0) return 1;
+               return (t == 0 && ((x.b->core.flag>>6&3) < (y.b->core.flag>>6&3)));
+       } else return 0;
+}
+
+KSORT_INIT(bamshuf, elem_t, elem_lt)
+
+static void bamshuf(const char *fn, int n_files, const char *pre, int clevel, int is_stdout)
+{
+       BGZF *fp, *fpw, **fpt;
+       char **fnt, modew[8];
+       bam1_t *b;
+       int i, l;
+       bam_hdr_t *h;
+       int64_t *cnt;
+
+       // split
+       fp = strcmp(fn, "-")? bgzf_open(fn, "r") : bgzf_dopen(fileno(stdin), "r");
+       assert(fp);
+       h = bam_hdr_read(fp);
+       fnt = (char**)calloc(n_files, sizeof(void*));
+       fpt = (BGZF**)calloc(n_files, sizeof(void*));
+       cnt = (int64_t*)calloc(n_files, 8);
+       l = strlen(pre);
+       for (i = 0; i < n_files; ++i) {
+               fnt[i] = (char*)calloc(l + 10, 1);
+               sprintf(fnt[i], "%s.%.4d.bam", pre, i);
+               fpt[i] = bgzf_open(fnt[i], "w1");
+               bam_hdr_write(fpt[i], h);
+       }
+       b = bam_init1();
+       while (bam_read1(fp, b) >= 0) {
+               uint32_t x;
+               x = hash_X31_Wang(bam_get_qname(b)) % n_files;
+               bam_write1(fpt[x], b);
+               ++cnt[x];
+       }
+       bam_destroy1(b);
+       for (i = 0; i < n_files; ++i) bgzf_close(fpt[i]);
+       free(fpt);
+       bgzf_close(fp);
+       // merge
+       sprintf(modew, "w%d", (clevel >= 0 && clevel <= 9)? clevel : DEF_CLEVEL);
+       if (!is_stdout) { // output to a file
+               char *fnw = (char*)calloc(l + 5, 1);
+               sprintf(fnw, "%s.bam", pre);
+               fpw = bgzf_open(fnw, modew);
+               free(fnw);
+       } else fpw = bgzf_dopen(fileno(stdout), modew); // output to stdout
+       bam_hdr_write(fpw, h);
+       bam_hdr_destroy(h);
+       for (i = 0; i < n_files; ++i) {
+               int64_t j, c = cnt[i];
+               elem_t *a;
+               fp = bgzf_open(fnt[i], "r");
+               bam_hdr_destroy(bam_hdr_read(fp));
+               a = (elem_t*)calloc(c, sizeof(elem_t));
+               for (j = 0; j < c; ++j) {
+                       a[j].b = bam_init1();
+                       assert(bam_read1(fp, a[j].b) >= 0);
+                       a[j].key = hash_X31_Wang(bam_get_qname(a[j].b));
+               }
+               bgzf_close(fp);
+               unlink(fnt[i]);
+               free(fnt[i]);
+               ks_introsort(bamshuf, c, a);
+               for (j = 0; j < c; ++j) {
+                       bam_write1(fpw, a[j].b);
+                       bam_destroy1(a[j].b);
+               }
+               free(a);
+       }
+       bgzf_close(fpw);
+       free(fnt); free(cnt);
+}
+
+int main_bamshuf(int argc, char *argv[])
+{
+       int c, n_files = 64, clevel = DEF_CLEVEL, is_stdout = 0, is_un = 0;
+       while ((c = getopt(argc, argv, "n:l:uO")) >= 0) {
+               switch (c) {
+               case 'n': n_files = atoi(optarg); break;
+               case 'l': clevel = atoi(optarg); break;
+               case 'u': is_un = 1; break;
+               case 'O': is_stdout = 1; break;
+               }
+       }
+       if (is_un) clevel = 0;
+       if (optind + 2 > argc) {
+               fprintf(stderr, "\nUsage:   bamshuf [-Ou] [-n nFiles] [-c cLevel] <in.bam> <out.prefix>\n\n");
+               fprintf(stderr, "Options: -O      output to stdout\n");
+               fprintf(stderr, "         -u      uncompressed BAM output\n");
+               fprintf(stderr, "         -l INT  compression level [%d]\n", DEF_CLEVEL);
+               fprintf(stderr, "         -n INT  number of temporary files [%d]\n", n_files);
+               fprintf(stderr, "\n");
+               return 1;
+       }
+       bamshuf(argv[optind], n_files, argv[optind+1], clevel, is_stdout);
+       return 0;
+}