[med-svn] [seqan2] 01/01: New upstream version 2.3.2.000platform-issues5-86390dc+dfsg

[Michael Crusoe]

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misterc-guest pushed a commit to annotated tag upstream/2.3.2.000platform-issues5-86390dc+dfsg
in repository seqan2.

commit e3580d1266ccefa38a81b177ab7ec2ae01816ca8
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date:   Wed Nov 8 06:58:20 2017 -0800

    New upstream version 2.3.2.000platform-issues5-86390dc+dfsg
---
 apps/yara/tests/run_tests.py         | 12 +++++++++---
 include/seqan/bam_io/bam_index_bai.h |  2 +-
 include/seqan/platform.h             |  2 +-
 3 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/apps/yara/tests/run_tests.py b/apps/yara/tests/run_tests.py
index 5dc3e5d..2fd875c 100644
--- a/apps/yara/tests/run_tests.py
+++ b/apps/yara/tests/run_tests.py
@@ -99,15 +99,21 @@ 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=[(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)])
+                to_diff=td)
             conf_list.append(conf)
 
     # ============================================================
diff --git a/include/seqan/bam_io/bam_index_bai.h b/include/seqan/bam_io/bam_index_bai.h
index 7aa7230..4a115f9 100644
--- a/include/seqan/bam_io/bam_index_bai.h
+++ b/include/seqan/bam_io/bam_index_bai.h
@@ -566,7 +566,7 @@ inline bool save(BamIndex<Bai> const & index, char const * baiFilename)
     typedef TBamIndex::TBinIndex_ const        TBinIndex;
     typedef TBinIndex::const_iterator          TBinIndexIter;
     typedef TBamIndex::TLinearIndex_           TLinearIndex;
-    for (int i = 0; i < numRefSeqs; ++i)
+    for (unsigned i = 0; i < length(index._binIndices); ++i)
     {
         TBinIndex const & binIndex = index._binIndices[i];
         TLinearIndex const & linearIndex = index._linearIndices[i];
diff --git a/include/seqan/platform.h b/include/seqan/platform.h
index 649f630..5bf0f5b 100644
--- a/include/seqan/platform.h
+++ b/include/seqan/platform.h
@@ -534,7 +534,7 @@ inline void ensure_little_endian(double & in)
 
 // DEFAULT PAGESIZE FOR MMAP
 #ifndef SEQAN_DEFAULT_PAGESIZE
-    #if SEQAN_IS_64_BIT
+    #if SEQAN_IS_64_BIT || defined(__powerpc__)
         #define SEQAN_DEFAULT_PAGESIZE 64 * 1024
     #else
         #define SEQAN_DEFAULT_PAGESIZE  4 * 1024

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