[med-svn] [bwa] 02/03: add patch to check avg and std for nan

[Nadiya Sitdykova]

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

commit 7722b0f5bb0e2f1d4ceea9ce0f2c6f695969995b
Author: Nadiya Sitdykova <rovenskasa at gmail.com>
Date:   Mon Jul 3 21:29:56 2017 -0400

    add patch to check avg and std for nan
---
 debian/changelog                   |  3 +++
 debian/patches/check_for_nan.patch | 17 +++++++++++++++++
 debian/patches/series              |  1 +
 3 files changed, 21 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index f3afc2d..7285634 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -6,6 +6,9 @@ bwa (0.7.15-5) UNRELEASED; urgency=medium
   * Add patch to fix heap block overrun 
   * Add patch with workaround for incorrect implicit type casting
     (resolves upstream issue #108) 
+  * Remove patch with workaround for issue #108
+  * Add patch that checks computed avg and std for nan
+    (straitforward fix for upstream issue #108)
 
   [Steffen Moeller]
   * debian/upstream/metadata: Added bio.tools entry
diff --git a/debian/patches/check_for_nan.patch b/debian/patches/check_for_nan.patch
new file mode 100644
index 0000000..73fd9fa
--- /dev/null
+++ b/debian/patches/check_for_nan.patch
@@ -0,0 +1,17 @@
+Author: Fabian Klötzl 
+Description: check computed avg and std for nan
+Last-Update: 2017-07-03
+Bug: https://github.com/lh3/bwa/issues/108
+===========================================================
+--- bwa.orig/bwtsw2_pair.c
++++ bwa/bwtsw2_pair.c
+@@ -85,6 +85,9 @@
+ 	if (r.high < r.avg + MAX_STDDEV * r.std) r.high = (int)(r.avg + MAX_STDDEV * r.std + .499);
+ 	ksprintf(msg, "[%s] low and high boundaries for proper pairs: (%d, %d)\n", __func__, r.low, r.high);
+ 	free(isize);
++	if (isnan(r.avg) || isnan(r.std)){
++		r.failed = 1;
++	}
+ 	return r;
+ }
+ 
diff --git a/debian/patches/series b/debian/patches/series
index f3cbd59..d6647f8 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
+check_for_nan.patch
 fix_heap_block_overrun
 fix_build_on_freebsd.patch
 check_number_of_arguments.patch

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