[med-svn] r17945 - trunk/packages/bowtie/trunk/debian

[Andreas Tille]

Author: tille
Date: 2014-09-05 09:31:56 +0000 (Fri, 05 Sep 2014)
New Revision: 17945

Modified:
   trunk/packages/bowtie/trunk/debian/README.Debian
   trunk/packages/bowtie/trunk/debian/changelog
Log:
Enhance documentation about testing and upload to unstable


Modified: trunk/packages/bowtie/trunk/debian/README.Debian
===================================================================
--- trunk/packages/bowtie/trunk/debian/README.Debian	2014-09-05 09:30:33 UTC (rev 17944)
+++ trunk/packages/bowtie/trunk/debian/README.Debian	2014-09-05 09:31:56 UTC (rev 17945)
@@ -1,6 +1,9 @@
 Bowtie for Debian
 =================
 
+1. Architecture dependency of bowtie
+------------------------------------
+
 Upstream has included an old copy of a gcc owned header file (cpuid.h).
 This should be generally considered a bad idea and it breaks compilation
 on other architectures than amd64 (most probably since a copy of the
@@ -12,8 +15,76 @@
     reportbug bowtie
 
 
-Hint from manual:
+2. Test suite for bowtie created and potential issue with sorting
+-----------------------------------------------------------------
 
+Regarding the difference in sorting order in example 5 of the manual
+there was some discussion on the Debian Med mailing list
+(https://lists.debian.org/debian-med/2014/09/msg00031.html) which is
+summarised here:
+
+
+Date: Wed, 3 Sep 2014 12:27:35 +0200
+From: Andreas Tille <andreas at an3as.eu>
+
+  $ bowtie -a --best -v 2 e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT
+ 
+  is supposed to have the output
+ 
+-       gi|110640213|ref|NC_008253.1|   2852852 8:T>A
++       gi|110640213|ref|NC_008253.1|   1093035 2:T>G,15:A>T
+-       gi|110640213|ref|NC_008253.1|   905664  6:A>G,7:G>T
+-       gi|110640213|ref|NC_008253.1|   148810  10:A>G,13:C>G
+-       gi|110640213|ref|NC_008253.1|   4930433 4:G>T,6:C>G
+ 
+  according to the manual but produces with the current arch-amd64
+  specific build in unstable as well as with the new build
+ 
+-       gi|110640213|ref|NC_008253.1|   2852852 8:T>A
+-       gi|110640213|ref|NC_008253.1|   148810  10:A>G,13:C>G
++       gi|110640213|ref|NC_008253.1|   1093035 2:T>G,15:A>T
+-       gi|110640213|ref|NC_008253.1|   905664  6:A>G,7:G>T
+-       gi|110640213|ref|NC_008253.1|   4930433 4:G>T,6:C>G
+ 
+
+Date: Thu, 04 Sep 2014 17:12:50 -0500
+From: Scott Christley <schristley at mac.com>:
+
+  Example 5: -a --best
+
+  "Specifying -a results in the same alignments being printed as if
+   just -a had been specified, but they are guaranteed to be reported
+   in best-to-worst order"
+
+  This would imply that the test failed, as the order of the output
+  matters.  BUT, and this is where it is unclear, what would be order
+  for "ties"?  The "best-to-worst" order is based upon the number of
+  mismatches and line 2-5 all have 2 mismatches (line 1 has 1 mismatch,
+  the 8:T>A, and thus is the best), i.e. they are all a tie.
+
+  From looking at the bowtie output you provided, the content is the same.
+  The sequence id names, position and mismatches are identical in both
+  outputs, the only difference is the order.  That may not even be
+  bowtie's fault, it may be using some system or other library which
+  does sorting slightly differently, and most specifically handling ties
+  differently.
+
+  My opinion, especially if you tried the other examples in the manual,
+  and those are okay, then you are okay with this fix, because it is seems
+  to be an arch-specific difference in sorting, whereby sorting is only
+  triggered with the --best option.
+
+
+As a consequence of this discussion it was decided to take the current
+result of the example 5 as the "expected result" of the test suite.  Any
+input about this is welcome to enhance the reliability of bowtie inside
+Debian.
+
+
+
+3. Further hint from manual which might increase performance
+------------------------------------------------------------
+
     If your computer has multiple processors/cores, use `-p`
 
     The `-p` option causes Bowtie to launch a specified number of

Modified: trunk/packages/bowtie/trunk/debian/changelog
===================================================================
--- trunk/packages/bowtie/trunk/debian/changelog	2014-09-05 09:30:33 UTC (rev 17944)
+++ trunk/packages/bowtie/trunk/debian/changelog	2014-09-05 09:31:56 UTC (rev 17945)
@@ -1,4 +1,4 @@
-bowtie (1.0.1-2) UNRELEASED; urgency=medium
+bowtie (1.0.1-2) unstable; urgency=medium
 
   * Do not use copy of outdated gcc header file which destroys portability
     to other architectures
@@ -7,6 +7,8 @@
     of cpuid.h
   * Add unit tests for build time and autopkgtest
   * Add debian/README.test to explain how to test the package
+    Attention: Please take notice of /usr/share/bowtie/README.Debian about
+      "Test suite for bowtie created and potential issue with sorting"
 
  -- Andreas Tille <tille at debian.org>  Wed, 03 Sep 2014 09:50:22 +0200