[med-svn] [bwa] 01/01: fix issues found within investigation of upstream issue #108

[Nadiya Sitdykova]

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rovenskasa-guest pushed a commit to branch master
in repository bwa.

commit 521729be5aef886451145b8fbd0e30c57a5eb184
Author: Nadiya Sitdykova <rovenskasa at gmail.com>
Date:   Fri Jun 30 17:42:56 2017 -0400

    fix issues found within investigation of upstream issue #108
---
 debian/changelog                      | 11 +++++++++++
 debian/patches/fix_heap_block_overrun | 18 ++++++++++++++++++
 debian/patches/fix_wrong_type_casting | 20 ++++++++++++++++++++
 debian/patches/series                 |  2 ++
 4 files changed, 51 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 8e932f8..d74824c 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,14 @@
+bwa (0.7.15-5) UNRELEASED; urgency=medium
+
+  * Team upload.
+  
+  [Nadiya Sitdykova]
+  * Add patch to fix heap block overrun 
+  * Add patch with workaround for incorrect implicit type casting
+    (resolves upstream issue #108) 
+
+ -- Nadiya Sitdykova <rovenskasa at gmail.com>  Fri, 30 Jun 2017 17:37:35 -0400
+
 bwa (0.7.15-4) UNRELEASED; urgency=medium
 
   * Debugging (see deactivated patch debian/patches/debug.patch that tries
diff --git a/debian/patches/fix_heap_block_overrun b/debian/patches/fix_heap_block_overrun
new file mode 100644
index 0000000..b572574
--- /dev/null
+++ b/debian/patches/fix_heap_block_overrun
@@ -0,0 +1,18 @@
+Author: Nadiya Sitdykova
+Description: allocate more memory so the heap block overrun wouldn't 
+happen (when qlen = 0). Issue was spotted by valgrind during 
+investigation of bug https://github.com/lh3/bwa/issues/108
+Last-Update: 2017-06-30
+
+======================================================================
+--- bwa.orig/ksw.c
++++ bwa/ksw.c
+@@ -385,7 +385,7 @@
+ 	assert(h0 > 0);
+ 	// allocate memory
+ 	qp = malloc(qlen * m);
+-	eh = calloc(qlen + 1, 8);
++	eh = calloc(qlen + 2, 8);
+ 	// generate the query profile
+ 	for (k = i = 0; k < m; ++k) {
+ 		const int8_t *p = &mat[k * m];
diff --git a/debian/patches/fix_wrong_type_casting b/debian/patches/fix_wrong_type_casting
new file mode 100644
index 0000000..d74baf8
--- /dev/null
+++ b/debian/patches/fix_wrong_type_casting
@@ -0,0 +1,20 @@
+Author: Nadiya Sitdykova
+Description: a workaround for incorrect implicit type casting. 
+The comparison end - beg < l_mseq incorrectly returned False 
+when end = 0, beg = 1, l_mseq = 149. Which led to further call 
+of malloc with negative argument.
+Last-Update: 2017-06-30
+Bug: https://github.com/lh3/bwa/issues/108
+
+=================================================================
+--- bwa.orig/bwtsw2_pair.c
++++ bwa/bwtsw2_pair.c
+@@ -117,7 +117,7 @@
+ 	}
+ 	if (beg < 1) beg = 1;
+ 	if (end > l_pac) end = l_pac;
+-	if (end - beg < l_mseq) return;
++	if (end < beg || end - beg < l_mseq) return;
+ 	// generate the sequence
+ 	seq = malloc(l_mseq + (end - beg));
+ 	ref = seq + l_mseq;
diff --git a/debian/patches/series b/debian/patches/series
index 205560e..d2dadad 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,5 @@
+fix_heap_block_overrun
+fix_wrong_type_casting
 fix_build_on_freebsd.patch
 check_number_of_arguments.patch
 spelling.patch

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