[med-svn] [hhsuite] 01/01: Specify correct format in printf statement

[Andreas Tille]

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tille pushed a commit to branch master
in repository hhsuite.

commit 9b1eca7c5560161e1ebd78b2dde6f92adff4e087
Author: Andreas Tille <tille at debian.org>
Date:   Wed Jan 18 16:52:25 2017 +0100

    Specify correct format in printf statement
---
 debian/changelog                                 |  8 +++++++
 debian/patches/fix_type_mismatch_in_printf.patch | 30 ++++++++++++++++++++++++
 debian/patches/series                            |  1 +
 3 files changed, 39 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 3e0ff88..c7ab302 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+hhsuite (3.0~beta2+dfsg-3) unstable; urgency=medium
+
+  * Specify correct format in printf statement (Thanks for the patch to
+    Daniel Shahaf <danielsh at apache.org>)
+    Closes: #851764
+
+ -- Andreas Tille <tille at debian.org>  Wed, 18 Jan 2017 16:52:21 +0100
+
 hhsuite (3.0~beta2+dfsg-2) unstable; urgency=medium
 
   * Really fix watch file to fetch latest version
diff --git a/debian/patches/fix_type_mismatch_in_printf.patch b/debian/patches/fix_type_mismatch_in_printf.patch
new file mode 100644
index 0000000..ab2d5df
--- /dev/null
+++ b/debian/patches/fix_type_mismatch_in_printf.patch
@@ -0,0 +1,30 @@
+Author: Daniel Shahaf  <danielsh at apache.org>
+Last-Update: Wed, Jan 18, 2017 at 15:22:26 +0000
+Bug-Debian: https://bugs.debian.org/851764
+Description: hhblits.cpp uses the %i printf(3) conversion to format a 'double' value
+ Thats undefined and prints garbage - the patch inserts the correct format
+ (and also fixes the doc about the correct default value
+
+--- a/doc/hhsuite-userguide.tex
++++ b/doc/hhsuite-userguide.tex
+@@ -1466,7 +1466,7 @@
+  -maxfilt                  max number of hits allowed to pass 2nd prefilter (default=20000)   
+  -min_prefilter_hits       min number of hits to pass prefilter (default=100)               
+  -prepre_smax_thresh       min score threshold of ungapped prefilter (default=10)               
+- -pre_evalue_thresh        max E-value threshold of Smith-Waterman prefilter score (default=0)
++ -pre_evalue_thresh        max E-value threshold of Smith-Waterman prefilter score (default=1000.0)
+  -pre_bitfactor            prefilter scores are in units of 1 bit / pre_bitfactor (default=4)
+  -pre_gap_open             gap open penalty in prefilter Smith-Waterman alignment (default=20)
+  -pre_gap_extend           gap extend penalty in prefilter Smith-Waterman alignment (default=4)
+--- a/src/hhblits.cpp
++++ b/src/hhblits.cpp
+@@ -330,7 +330,7 @@
+     printf(" -maxfilt                  max number of hits allowed to pass 2nd prefilter (default=%i)   \n", par.maxnumdb);
+     printf(" -min_prefilter_hits       min number of hits to pass prefilter (default=%i)               \n", par.min_prefilter_hits);
+     printf(" -prepre_smax_thresh       min score threshold of ungapped prefilter (default=%i)               \n", par.preprefilter_smax_thresh);
+-    printf(" -pre_evalue_thresh        max E-value threshold of Smith-Waterman prefilter score (default=%i)\n", par.prefilter_evalue_thresh);
++    printf(" -pre_evalue_thresh        max E-value threshold of Smith-Waterman prefilter score (default=%.1f)\n", par.prefilter_evalue_thresh);
+     printf(" -pre_bitfactor            prefilter scores are in units of 1 bit / pre_bitfactor (default=%i)\n", par.prefilter_bit_factor);
+     printf(" -pre_gap_open             gap open penalty in prefilter Smith-Waterman alignment (default=%i)\n", par.prefilter_gap_open);
+     printf(" -pre_gap_extend           gap extend penalty in prefilter Smith-Waterman alignment (default=%i)\n", par.prefilter_gap_extend);
+
diff --git a/debian/patches/series b/debian/patches/series
index ae933a6..1a22412 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -8,3 +8,4 @@ drop-fmemopen.h.patch
 build-own-manual-PDF.patch
 set-default-HHLIB-dir.patch
 disable-AVX-SSE.patch
+fix_type_mismatch_in_printf.patch

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