[med-svn] samtools 04/07: Removed fix_coverage_cap.patch, obsoleted by -d option.

[Charles Plessy]

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

commit 23e44a4110a57524a37a013e8eedf3bbc37c9541
Author: Charles Plessy <plessy at debian.org>
Date:   Mon Jun 15 21:44:28 2015 +0900

    Removed fix_coverage_cap.patch, obsoleted by -d option.
    
    See https://github.com/samtools/samtools/issues/284
---
 debian/patches/fix_coverage_cap.patch | 13 -------------
 debian/patches/series                 |  1 -
 2 files changed, 14 deletions(-)

diff --git a/debian/patches/fix_coverage_cap.patch b/debian/patches/fix_coverage_cap.patch
deleted file mode 100644
index aa27e33..0000000
--- a/debian/patches/fix_coverage_cap.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-Description: increases the coverage cap from 8.000 to 1.000.000
-Forwarded: https://github.com/samtools/samtools/issues/284
-
---- 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(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
diff --git a/debian/patches/series b/debian/patches/series
index 74ed30a..dda8ba0 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,2 @@
-fix_coverage_cap.patch
 fix_segfault_with_small_ref.patch
 dynamic-build.patch

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