[med-svn] [seqan2] 01/01: New upstream version 2.3.2.000platform-issues6-9cf5a69+dfsg

[Michael Crusoe]

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misterc-guest pushed a commit to annotated tag upstream/2.3.2.000platform-issues6-9cf5a69+dfsg
in repository seqan2.

commit c1d8a216f17856548d87ef3e9f017f34452e1e46
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date:   Sat Nov 11 05:40:26 2017 -0800

    New upstream version 2.3.2.000platform-issues6-9cf5a69+dfsg
---
 apps/yara/tests/run_tests.py           | 28 +++++++++++-----------------
 tests/bam_io/test_bam_sam_conversion.h |  4 +++-
 2 files changed, 14 insertions(+), 18 deletions(-)

diff --git a/apps/yara/tests/run_tests.py b/apps/yara/tests/run_tests.py
index 2fd875c..fd518a5 100644
--- a/apps/yara/tests/run_tests.py
+++ b/apps/yara/tests/run_tests.py
@@ -33,6 +33,12 @@ sam_transforms = [
 def main(source_base, binary_base):
     """Main entry point of the script."""
 
+    # gold standard binary files created on little endian
+    if sys.byteorder != 'little':
+        print 'Skipping tests for Yara on big endian'
+        print '====================================='
+        return 0
+
     print 'Executing test for Yara'
     print '=============================='
     print
@@ -69,18 +75,12 @@ def main(source_base, binary_base):
         exts = [os.path.basename(fname).split('.', 1)[-1]
                 for fname in glob.glob(ph.inFile('gold/%s-genome.*' % organism))]
 
-        # gold standard binary files created on little endian
-        if sys.byteorder != 'little':
-            td = []
-        else:
-            td = [(ph.inFile('gold/%s-genome.%s' % (organism, ext)),
-                   ph.outFile('%s-genome.%s' % (organism, ext)), 'md5') for ext in exts]
-
         conf = app_tests.TestConf(
             program=path_to_indexer,
             args=[ph.inFile('input/%s-genome.fa' % organism),
                 '-o', ph.outFile('%s-genome' % organism)],
-            to_diff=td)
+            to_diff=[(ph.inFile('gold/%s-genome.%s' % (organism, ext)),
+                      ph.outFile('%s-genome.%s' % (organism, ext)), 'md5') for ext in exts])
         conf_list.append(conf)
 
     # ============================================================
@@ -99,21 +99,15 @@ def main(source_base, binary_base):
     for organism in ['adeno']:
         for i in range(0, len(mapper_args)):
 
-            # gold standard sam files are off due to rounding on big endian
-            if sys.byteorder != 'little':
-                td = []
-            else:
-                td = [(ph.inFile('gold/%s-reads_1.%s.sam' % (organism, mapper_suffix[i])),
-                       ph.outFile('%s-reads_1.%s.sam' % (organism, mapper_suffix[i])),
-                       sam_transforms)]
-
             conf = app_tests.TestConf(
                 program=path_to_mapper,
                 args=[ph.inFile('gold/%s-genome' % organism),
                       ph.inFile('input/%s-reads_1.fa' % organism),
                       '-o', ph.outFile('%s-reads_1.%s.sam' % (organism, mapper_suffix[i]))] +
                       mapper_args[i],
-                to_diff=td)
+                to_diff=[(ph.inFile('gold/%s-reads_1.%s.sam' % (organism, mapper_suffix[i])),
+                          ph.outFile('%s-reads_1.%s.sam' % (organism, mapper_suffix[i])),
+                          sam_transforms)])
             conf_list.append(conf)
 
     # ============================================================
diff --git a/tests/bam_io/test_bam_sam_conversion.h b/tests/bam_io/test_bam_sam_conversion.h
index 2510072..176c121 100644
--- a/tests/bam_io/test_bam_sam_conversion.h
+++ b/tests/bam_io/test_bam_sam_conversion.h
@@ -298,7 +298,9 @@ SEQAN_DEFINE_TEST(test_assign_tags_sam_to_bam_type_f)
     resize(expected, 7);
     char const * DATA = "XXf\x00\x00\x00\x3f";
     arrayCopy(DATA, DATA + 7, begin(expected, Standard()));
-    SEQAN_ASSERT(startsWith(CharString(bamTags), expected));
+#if !SEQAN_BIG_ENDIAN // floating point madness
+    SEQAN_ASSERT_EQ(expected, CharString(bamTags));
+#endif
 }
 
 SEQAN_DEFINE_TEST(test_assign_tags_sam_to_bam_type_Z)

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