[med-svn] [bwa] 01/02: Drop debugging output

[Andreas Tille]

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tille pushed a commit to branch master
in repository bwa.

commit 6bd929d4960029a9b6615bb0a3380fe12fae06c9
Author: Andreas Tille <tille at debian.org>
Date:   Mon Jul 17 15:21:06 2017 +0200

    Drop debugging output
---
 debian/patches/debug.patch | 30 ------------------------------
 debian/patches/series      |  1 -
 2 files changed, 31 deletions(-)

diff --git a/debian/patches/debug.patch b/debian/patches/debug.patch
deleted file mode 100644
index 4cdb9e8..0000000
--- a/debian/patches/debug.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Thu, 16 Mar 2017 09:12:09 +0100
-Description: Try to address https://github.com/lh3/bwa/issues/108
- BWA is crashing reproducibly on different computers in
-      seq[l_mseq - 1 - i] = c > 3? 4 : 3 - c;
- but at different states of data.  No idea what might be wrong here.
-
---- a/bwtsw2_pair.c
-+++ b/bwtsw2_pair.c
-@@ -119,15 +119,19 @@ void bsw2_pair1(const bsw2opt_t *opt, in
- 	if (end > l_pac) end = l_pac;
- 	if (end - beg < l_mseq) return;
- 	// generate the sequence
--	seq = malloc(l_mseq + (end - beg));
-+fprintf(stderr, "%s(%i): l_mseq = %i, end = %i, beg = %i, allocating %i\n", __FILE__, __LINE__, l_mseq, end, beg, l_mseq + (end - beg)); fflush( stderr );
-+	seq = malloc(l_mseq + (end - beg) + 1);
- 	ref = seq + l_mseq;
- 	for (k = beg; k < end; ++k)
- 		ref[k - beg] = pac[k>>2] >> ((~k&3)<<1) & 0x3;
- 	if (h->is_rev == 0) {
-+fprintf(stderr, "%s(%i): l_mseq = %i\n", __FILE__, __LINE__, l_mseq); fflush( stderr );
- 		for (i = 0; i < l_mseq; ++i) { // on the reverse strand
- 			int c = nst_nt4_table[(int)mseq[i]];
-+fprintf(stderr, "%s(%i): i=%i, l_mseq = %i, c=%i, writing to position: l_mseq - 1 - i = %i\n", __FILE__, __LINE__, i, l_mseq, c, l_mseq - 1 - i); fflush( stderr );
- 			seq[l_mseq - 1 - i] = c > 3? 4 : 3 - c;
- 		}
-+fprintf(stderr, "%s(%i): i = %i\n", __FILE__, __LINE__, i); fflush( stderr );
- 	} else {
- 		for (i = 0; i < l_mseq; ++i) // on the forward strand
- 			seq[i] = nst_nt4_table[(int)mseq[i]];
diff --git a/debian/patches/series b/debian/patches/series
index dd0ee4e..6687ece 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -4,4 +4,3 @@ fix_heap_block_overrun
 fix_build_on_freebsd.patch
 check_number_of_arguments.patch
 spelling.patch
-debug.patch

-- 
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