update cl/fmt for release

Illumina · Apr 27, 2015 · f8e6b8d · f8e6b8d
1 parent 9f084d3
commit f8e6b8d
Show file tree

Hide file tree

Showing 8 changed files with 27 additions and 24 deletions.
diff --git a/ChangeLog.txt b/ChangeLog.txt
@@ -1,4 +1,5 @@
-- MANTA-224 improve short-fragment handling for RNA 
+v0.26.0
+- MANTA-224 improve short-fragment handling for RNA
 - MANTA-235 kmer refernce mask to accelerate RNA contig alignments
 - MANTA-232 filter large SVs with no read pair support
 - MANTA-236 expand conditions for large insertion search to normalize

diff --git a/src/c++/lib/applications/EstimateSVLoci/ESLOptions.cpp b/src/c++/lib/applications/EstimateSVLoci/ESLOptions.cpp
@@ -84,7 +84,7 @@ parseESLOptions(
      "samtools formatted region, eg. 'chr1:20-30'")
     ("rna", po::value(&opt.isRNA)->zero_tokens(),
      "For RNA input. Changes small fragment handling.")
-     ;
+    ;
 
     po::options_description alignDesc(getOptionsDescription(opt.alignFileOpt));
     po::options_description scanDesc(getOptionsDescription(opt.scanOpt));

diff --git a/src/c++/lib/applications/GenerateSVCandidates/SVCandidateAssemblyRefiner.cpp b/src/c++/lib/applications/GenerateSVCandidates/SVCandidateAssemblyRefiner.cpp
@@ -1151,7 +1151,7 @@ bool translateMaskedAlignment(
         else
         {
             const unsigned length = translateMaskedPos(exclBlocks, cpos + seg.length) -
-                    translateMaskedPos(exclBlocks, cpos);
+                                    translateMaskedPos(exclBlocks, cpos);
             if (is_segment_align_match(seg.type) && (length != seg.length)) return false;
 #ifdef DEBUG_KMER
             log_os << __FUNCTION__ << " SEGMENT " << seg.type << " " << seg.length << "\n";
@@ -1176,11 +1176,11 @@ bool translateMaskedAlignment(
 /// Returns a reduced reference sequence where long stretches without kmer matches to the contig are removed
 template <typename SymIter>
 std::string kmerMaskReference(
-               const SymIter refSeqStart, 
-               const SymIter refSeqEnd,
-               const std::string& contig,
-               const int nSpacer,
-               std::vector<exclusion_block>& exclBlocks)
+    const SymIter refSeqStart,
+    const SymIter refSeqEnd,
+    const std::string& contig,
+    const int nSpacer,
+    std::vector<exclusion_block>& exclBlocks)
 {
     // Hash all kmers in the contig
     static const int merSize(10);
@@ -1510,16 +1510,16 @@ getJumpAssembly(
         {
 #ifdef DEBUG_REFINER
             log_os << __FUNCTION__ << " RNA alignment\n";
-#endif           
+#endif
             static const int nSpacer(25);
             std::vector<exclusion_block> exclBlocks1;
             const std::string cutRef1 = kmerMaskReference(align1RefStrPtr->begin() + align1LeadingCut,
-                    align1RefStrPtr->end() - align1TrailingCut, 
-                    contig.seq, nSpacer, exclBlocks1);
+                                                          align1RefStrPtr->end() - align1TrailingCut,
+                                                          contig.seq, nSpacer, exclBlocks1);
             std::vector<exclusion_block> exclBlocks2;
             const std::string cutRef2 = kmerMaskReference(align2RefStrPtr->begin() + align2LeadingCut,
-                    align2RefStrPtr->end() - align2TrailingCut,
-                    contig.seq, nSpacer, exclBlocks2);
+                                                          align2RefStrPtr->end() - align2TrailingCut,
+                                                          contig.seq, nSpacer, exclBlocks2);
 #ifdef DEBUG_REFINER
             log_os << __FUNCTION__ << " Kmer-masked references\n";
             log_os << "\t ref Lengths " << align1RefStrPtr->size() << " " << align2RefStrPtr->size() << "\n";
@@ -1532,16 +1532,16 @@ getJumpAssembly(
             log_os << __FUNCTION__ << ": bp1Fw: " << bp1Fw << " ; bp2Fw: " << bp2Fw << '\n';
 #endif
             _RNASpanningAligner.align(contig.seq.begin(), contig.seq.end(),
-                    cutRef1.begin(), cutRef1.end(), cutRef2.begin(), cutRef2.end(),
-                    bp1Fw, bp2Fw,
-                    alignment);
-            
+                                      cutRef1.begin(), cutRef1.end(), cutRef2.begin(), cutRef2.end(),
+                                      bp1Fw, bp2Fw,
+                                      alignment);
+
 #ifdef DEBUG_REFINER
             log_os << __FUNCTION__ << " Masked 1: " << alignment.align1 << '\n';
             log_os << __FUNCTION__ << " Masked 2: " << alignment.align2 << '\n';
 #endif
             if (!(translateMaskedAlignment(alignment.align1, exclBlocks1) &&
-                translateMaskedAlignment(alignment.align2, exclBlocks2)))
+                  translateMaskedAlignment(alignment.align2, exclBlocks2)))
             {
 #ifdef DEBUG_REFINER
                 log_os << __FUNCTION__ << " Failed to fix kmer-masked alignment\n";

diff --git a/src/c++/lib/applications/GenerateSVCandidates/SVScorerSplit.cpp b/src/c++/lib/applications/GenerateSVCandidates/SVScorerSplit.cpp
@@ -188,8 +188,8 @@ scoreSplitReads(
     // We are not looking for remote reads, (semialigned-) reads mapping near this breakpoint, but not across it
     // or any other kind of additional reads used for assembly.
     readStream.set_new_region(bp.interval.tid,
-        std::max(0, bp.interval.range.begin_pos() - extendedSearchRange),
-        bp.interval.range.end_pos() + extendedSearchRange);
+                              std::max(0, bp.interval.range.begin_pos() - extendedSearchRange),
+                              bp.interval.range.end_pos() + extendedSearchRange);
     while (readStream.next())
     {
         const bam_record& bamRead(*(readStream.get_record_ptr()));

diff --git a/src/c++/lib/format/VcfWriterSV.cpp b/src/c++/lib/format/VcfWriterSV.cpp
@@ -831,7 +831,8 @@ writeSVCore(
         BOOST_THROW_EXCEPTION(LogicException(oss.str()));
     }
 
-    try {
+    try
+    {
         if      (isSVTransloc(svType))
         {
             writeTranslocPair(sv, svId, svData, adata, event);

diff --git a/src/c++/lib/manta/SVLocusScanner.cpp b/src/c++/lib/manta/SVLocusScanner.cpp
@@ -1353,7 +1353,7 @@ isSemiAlignedEvidence(
 {
     unsigned leadingMismatchLen(0), trailingMismatchLen(0);
     getSVBreakendCandidateSemiAlignedSimple(bamRead, bamAlign, refSeq, _dopt.isUseOverlappingPairs,
-                                      leadingMismatchLen, trailingMismatchLen);
+                                            leadingMismatchLen, trailingMismatchLen);
     return ((leadingMismatchLen >= _opt.minSemiAlignedMismatchLen) || (trailingMismatchLen >= _opt.minSemiAlignedMismatchLen));
 }
 

diff --git a/src/c++/lib/manta/SVLocusScanner.hh b/src/c++/lib/manta/SVLocusScanner.hh
@@ -111,7 +111,8 @@ struct SVLocusScanner
     {
         if      (bamRead.is_filter()) return true;
         else if (bamRead.is_dup()) return true;
-        else {
+        else
+        {
             // hack to work with bwamem '-M' formatting,
             // keep secondary reads when they contain an SA tag
             if (bamRead.is_secondary())

diff --git a/src/cmake/cxxTestLibrary.cmake b/src/cmake/cxxTestLibrary.cmake
@@ -39,7 +39,7 @@ endif ()
 if (WIN32)
     # create a fake library target on win32 instead of linking and running the unit test
     # this creates a project in VS that allows for interaction with the unit test code
-    
+
     # add all files to TEST_SOURCE to make the IDE project more usable:
     file(GLOB TMP_TARGET_FILES *)