From: Heng Li <lh3@me.com>
Date: Fri, 30 Mar 2012 02:27:57 +0000 (-0400)
Subject: shrink bam1_t::m_data when sorting
X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=0f2614cfa1db19990246c91e776ca280213d1940

shrink bam1_t::m_data when sorting

Otherwise most of allocated memory may not be used
---

diff --git a/bam.h b/bam.h
index 11f8028..efc0459 100644
--- a/bam.h
+++ b/bam.h
@@ -40,7 +40,7 @@
   @copyright Genome Research Ltd.
  */
 
-#define BAM_VERSION "0.1.18-dev (r982:313)"
+#define BAM_VERSION "0.1.18-master-r567"
 
 #include <stdint.h>
 #include <stdlib.h>
diff --git a/bam_sort.c b/bam_sort.c
index c451dcf..7d00cd1 100644
--- a/bam_sort.c
+++ b/bam_sort.c
@@ -472,6 +472,11 @@ void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size
 		if (buf[k] == 0) buf[k] = (bam1_t*)calloc(1, sizeof(bam1_t));
 		b = buf[k];
 		if ((ret = bam_read1(fp, b)) < 0) break;
+		if (b->data_len < b->m_data>>2) { // shrink
+			b->m_data = b->data_len;
+			kroundup32(b->m_data);
+			b->data = realloc(b->data, b->m_data);
+		}
 		mem += sizeof(bam1_t) + b->m_data + sizeof(void*) + sizeof(void*); // two sizeof(void*) for the data allocated to pointer arrays
 		++k;
 		if (mem >= max_mem) {