[med-svn] [bwa] 01/02: Leads to a different error than with more debugging lines: Thread 5 "bwa" received signal SIGSEGV, Segmentation fault. [Switching to Thread 0x7ffff285c700 (LWP 28547)] strlen () at ../sysdeps/x86_64/strlen.S:106 106 ../sysdeps/x86_64/strlen.S: No such file or directory.

[Andreas Tille]

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tille pushed a commit to branch master
in repository bwa.

commit af2b2665ab651e70d84dd1fda4e70202ab11e13f
Author: Andreas Tille <tille at debian.org>
Date:   Thu Mar 16 10:51:40 2017 +0100

    Leads to a different error than with more debugging lines:
    Thread 5 "bwa" received signal SIGSEGV, Segmentation fault.
    [Switching to Thread 0x7ffff285c700 (LWP 28547)]
    strlen () at ../sysdeps/x86_64/strlen.S:106
    106     ../sysdeps/x86_64/strlen.S: No such file or directory.
---
 debian/patches/debug.patch | 23 +++++++++++++++++++++++
 debian/patches/series      |  1 +
 2 files changed, 24 insertions(+)

diff --git a/debian/patches/debug.patch b/debian/patches/debug.patch
new file mode 100644
index 0000000..032e94d
--- /dev/null
+++ b/debian/patches/debug.patch
@@ -0,0 +1,23 @@
+--- 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 %s\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 ea8465e..205560e 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
 fix_build_on_freebsd.patch
 check_number_of_arguments.patch
 spelling.patch
+debug.patch

-- 
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