[med-svn] samtools 01/02: Refreshed for upstream version 1.0.

[Charles Plessy]

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plessy pushed a commit to branch debian/unstable
in repository samtools.

commit f73d7648351c785a378cc8affd52b872c2b4629b
Author: Charles Plessy <plessy at debian.org>
Date:   Thu Aug 21 08:19:40 2014 +0900

    Refreshed for upstream version 1.0.
---
 debian/patches/fix_coverage_cap.patch | 20 +++++++++-----------
 1 file changed, 9 insertions(+), 11 deletions(-)

diff --git a/debian/patches/fix_coverage_cap.patch b/debian/patches/fix_coverage_cap.patch
index d9c03aa..aa27e33 100644
--- a/debian/patches/fix_coverage_cap.patch
+++ b/debian/patches/fix_coverage_cap.patch
@@ -1,15 +1,13 @@
 Description: increases the coverage cap from 8.000 to 1.000.000
 Forwarded: https://github.com/samtools/samtools/issues/284
 
-Index: samtools/bam2depth.c
-===================================================================
---- samtools.orig/bam2depth.c
-+++ samtools/bam2depth.c
-@@ -106,6 +106,7 @@
+--- a/bam2depth.c
++++ b/bam2depth.c
+@@ -154,6 +154,7 @@
  
- 	// the core multi-pileup loop
- 	mplp = bam_mplp_init(n, read_bam, (void**)data); // initialization
-+	bam_mplp_set_maxcnt(mplp,1000000); // set maxdepth to 1M
- 	n_plp = calloc(n, sizeof(int)); // n_plp[i] is the number of covering reads from the i-th BAM
- 	plp = calloc(n, sizeof(void*)); // plp[i] points to the array of covering reads (internal in mplp)
- 	while (bam_mplp_auto(mplp, &tid, &pos, n_plp, plp) > 0) { // come to the next covered position
+     // the core multi-pileup loop
+     mplp = bam_mplp_init(n, read_bam, (void**)data); // initialization
++    bam_mplp_set_maxcnt(mplp,1000000); // set maxdepth to 1M
+     n_plp = calloc(n, sizeof(int)); // n_plp[i] is the number of covering reads from the i-th BAM
+     plp = calloc(n, sizeof(bam_pileup1_t*)); // plp[i] points to the array of covering reads (internal in mplp)
+     while (bam_mplp_auto(mplp, &tid, &pos, n_plp, plp) > 0) { // come to the next covered position

-- 
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