[med-svn] [seqan2] 01/01: New upstream version 2.3.2.000platform-issues2-206d1f7+dfsg

[Michael Crusoe]

This is an automated email from the git hooks/post-receive script.

misterc-guest pushed a commit to annotated tag upstream/2.3.2.000platform-issues2-206d1f7+dfsg
in repository seqan2.

commit 23692a211728258172b126325c1e883fc58bd71b
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date:   Thu Oct 26 05:13:29 2017 -0700

    New upstream version 2.3.2.000platform-issues2-206d1f7+dfsg
---
 apps/yara/tests/run_tests.py             | 12 +++++++++---
 include/seqan/parallel/parallel_lock.h   |  2 ++
 include/seqan/platform.h                 | 11 ++++++++++-
 include/seqan/stream/file_stream.h       |  2 +-
 include/seqan/stream/stream_compressor.h | 22 ++++++++++++++--------
 5 files changed, 36 insertions(+), 13 deletions(-)

diff --git a/apps/yara/tests/run_tests.py b/apps/yara/tests/run_tests.py
index ba87e82..5dc3e5d 100644
--- a/apps/yara/tests/run_tests.py
+++ b/apps/yara/tests/run_tests.py
@@ -69,12 +69,18 @@ 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=[(ph.inFile('gold/%s-genome.%s' % (organism, ext)),
-                     ph.outFile('%s-genome.%s' % (organism, ext)), 'md5') for ext in exts])
+                '-o', ph.outFile('%s-genome' % organism)],
+            to_diff=td)
         conf_list.append(conf)
 
     # ============================================================
diff --git a/include/seqan/parallel/parallel_lock.h b/include/seqan/parallel/parallel_lock.h
index 54f6a44..92126bf 100644
--- a/include/seqan/parallel/parallel_lock.h
+++ b/include/seqan/parallel/parallel_lock.h
@@ -215,6 +215,8 @@ yieldProcessor()
 {
 #if defined(STDLIB_VS)  // Visual Studio - all platforms.
     YieldProcessor();
+#elif defined(__armel__) || defined(__ARMEL__) // arm, but broken
+    asm volatile ("nop" ::: "memory");  // default operation - does nothing => Might lead to passive spinning.
 #elif defined(__arm__) || defined(__aarch64__)  // ARM.
     __asm__ __volatile__ ("yield" ::: "memory");
 #elif defined(__sparc) // SPARC
diff --git a/include/seqan/platform.h b/include/seqan/platform.h
index 365f5de..accaeab 100644
--- a/include/seqan/platform.h
+++ b/include/seqan/platform.h
@@ -488,7 +488,7 @@ template <typename T>
 constexpr void ensure_little_endian(T &)
 {}
 
-#if !SEQAN_BIG_ENDIAN
+#if SEQAN_BIG_ENDIAN
 inline void ensure_little_endian(int16_t & in)
 {
     in = htole16(in);
@@ -527,4 +527,13 @@ inline void ensure_little_endian(double & in)
 }
 #endif // SEQAN_BIG_ENDIAN
 
+// DEFAULT PAGESIZE FOR MMAP
+#ifndef SEQAN_DEFAULT_PAGESIZE
+    #if SEQAN_IS_64_BIT
+        #define SEQAN_DEFAULT_PAGESIZE 64 * 1024
+    #else
+        #define SEQAN_DEFAULT_PAGESIZE  4 * 1024
+    #endif
+#endif
+
 #endif // HEADER GUARD
diff --git a/include/seqan/stream/file_stream.h b/include/seqan/stream/file_stream.h
index 1cd43f7..e640086 100644
--- a/include/seqan/stream/file_stream.h
+++ b/include/seqan/stream/file_stream.h
@@ -178,7 +178,7 @@ clear(FilePage<TValue, TSpec> & me)
 // Class FilePager
 // ----------------------------------------------------------------------------
 
-template <unsigned SEQAN_PAGESIZE = 4 * 1024>
+template <unsigned SEQAN_PAGESIZE = SEQAN_DEFAULT_PAGESIZE>
 struct FixedPagingScheme
 {
     enum { pageSize = SEQAN_PAGESIZE };
diff --git a/include/seqan/stream/stream_compressor.h b/include/seqan/stream/stream_compressor.h
index e39e9ce..e820b4b 100644
--- a/include/seqan/stream/stream_compressor.h
+++ b/include/seqan/stream/stream_compressor.h
@@ -276,16 +276,20 @@ compress(TTarget & target, TSourceIterator & source, CompressionContext<BgzfFile
 // Helper Function _bgzfUnpackXX()
 // ----------------------------------------------------------------------------
 
-inline unsigned short
+inline uint16_t
 _bgzfUnpack16(char const * buffer)
 {
-    return *reinterpret_cast<unsigned short const *>(buffer);
+    uint16_t tmp = *reinterpret_cast<uint16_t const *>(buffer);
+    ensure_little_endian(tmp);
+    return tmp;
 }
 
-inline unsigned
+inline uint32_t
 _bgzfUnpack32(char const * buffer)
 {
-    return *reinterpret_cast<unsigned const *>(buffer);
+    uint32_t tmp = *reinterpret_cast<uint32_t const *>(buffer);
+    ensure_little_endian(tmp);
+    return tmp;
 }
 
 // ----------------------------------------------------------------------------
@@ -293,15 +297,17 @@ _bgzfUnpack32(char const * buffer)
 // ----------------------------------------------------------------------------
 
 inline void
-_bgzfPack16(char * buffer, unsigned short value)
+_bgzfPack16(char * buffer, uint16_t value)
 {
-    *reinterpret_cast<unsigned short *>(buffer) = value;
+    ensure_little_endian(value);
+    *reinterpret_cast<uint16_t *>(buffer) = value;
 }
 
 inline void
-_bgzfPack32(char * buffer, unsigned value)
+_bgzfPack32(char * buffer, uint32_t value)
 {
-    *reinterpret_cast<unsigned *>(buffer) = value;
+    ensure_little_endian(value);
+    *reinterpret_cast<uint32_t *>(buffer) = value;
 }
 
 

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/seqan2.git