From 7f4fd36b7000c9f19c249ebb0a127ed42f8eaec1 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Sun, 18 Mar 2012 14:46:00 -0400
Subject: [PATCH] added mt comression to merge
---
bam_sort.c | 17 ++++++++++++-----
sam_view.c | 1 +
2 files changed, 13 insertions(+), 5 deletions(-)
diff --git a/bam_sort.c b/bam_sort.c
index 2c2b83d..f436fb9 100644
--- a/bam_sort.c
+++ b/bam_sort.c
@@ -89,8 +89,7 @@ static void swap_header_text(bam_header_t *h1, bam_header_t *h2)
@discussion Padding information may NOT correctly maintained. This
function is NOT thread safe.
*/
-int bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn,
- int flag, const char *reg)
+int bam_merge_core2(int by_qname, const char *out, const char *headers, int n, char * const *fn, int flag, const char *reg, int n_threads)
{
bamFile fpout, *fp;
heap1_t *heap;
@@ -222,6 +221,7 @@ int bam_merge_core(int by_qname, const char *out, const char *headers, int n, ch
}
bam_header_write(fpout, hout);
bam_header_destroy(hout);
+ if (!(flag & MERGE_UNCOMP)) bgzf_mt(fpout, n_threads, 256);
ks_heapmake(heap, n, heap);
while (heap->pos != HEAP_EMPTY) {
@@ -256,12 +256,17 @@ int bam_merge_core(int by_qname, const char *out, const char *headers, int n, ch
return 0;
}
+int bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn, int flag, const char *reg)
+{
+ return bam_merge_core2(by_qname, out, headers, n, fn, flag, reg, 0);
+}
+
int bam_merge(int argc, char *argv[])
{
- int c, is_by_qname = 0, flag = 0, ret = 0;
+ int c, is_by_qname = 0, flag = 0, ret = 0, n_threads = 0;
char *fn_headers = NULL, *reg = 0;
- while ((c = getopt(argc, argv, "h:nru1R:f")) >= 0) {
+ while ((c = getopt(argc, argv, "h:nru1R:f@:")) >= 0) {
switch (c) {
case 'r': flag |= MERGE_RG; break;
case 'f': flag |= MERGE_FORCE; break;
@@ -270,6 +275,7 @@ int bam_merge(int argc, char *argv[])
case '1': flag |= MERGE_LEVEL1; break;
case 'u': flag |= MERGE_UNCOMP; break;
case 'R': reg = strdup(optarg); break;
+ case '@': n_threads = atoi(optarg); break;
}
}
if (optind + 2 >= argc) {
@@ -280,6 +286,7 @@ int bam_merge(int argc, char *argv[])
fprintf(stderr, " -u uncompressed BAM output\n");
fprintf(stderr, " -f overwrite the output BAM if exist\n");
fprintf(stderr, " -1 compress level 1\n");
+ fprintf(stderr, " -@ INT number of BAM compression threads [0]\n");
fprintf(stderr, " -R STR merge file in the specified region STR [all]\n");
fprintf(stderr, " -h FILE copy the header in FILE to <out.bam> [in1.bam]\n\n");
fprintf(stderr, "Note: Samtools' merge does not reconstruct the @RG dictionary in the header. Users\n");
@@ -295,7 +302,7 @@ int bam_merge(int argc, char *argv[])
return 1;
}
}
- if (bam_merge_core(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1, flag, reg) < 0) ret = 1;
+ if (bam_merge_core2(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1, flag, reg, n_threads) < 0) ret = 1;
free(reg);
free(fn_headers);
return ret;
diff --git a/sam_view.c b/sam_view.c
index f198591..b6896c9 100644
--- a/sam_view.c
+++ b/sam_view.c
@@ -290,6 +290,7 @@ static int usage(int is_long_help)
fprintf(stderr, " -X output FLAG in string (samtools-C specific)\n");
fprintf(stderr, " -c print only the count of matching records\n");
fprintf(stderr, " -B collapse the backward CIGAR operation\n");
+ fprintf(stderr, " -@ INT number of BAM compression threads [0]\n");
fprintf(stderr, " -L FILE output alignments overlapping the input BED FILE [null]\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");
--
2.39.5