MANTA-259 update cl and fmt

Illumina · Sep 14, 2015 · a7c1364 · a7c1364
1 parent 7fd1e4f
commit a7c1364
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Showing 12 changed files with 35 additions and 34 deletions.
diff --git a/ChangeLog.txt b/ChangeLog.txt
@@ -1,4 +1,5 @@
-- MANTA-259
+v0.28.0
+- MANTA-259 Support joint analysis of multiple diploid samples
 - MANTA-260 Add per-sample filtration to separate QUAL and GQ filters for
 diploid case
 - MANTA-252 Add fast chrom median depth estimator (partally enables CRAM)

diff --git a/src/c++/lib/applications/EstimateSVLoci/SVLocusSetFinder.cpp b/src/c++/lib/applications/EstimateSVLoci/SVLocusSetFinder.cpp
@@ -99,7 +99,7 @@ SVLocusSetFinder(
     const unsigned sampleCount(opt.alignFileOpt.alignmentFilename.size());
     _svLoci.getCounts().setSampleCount(sampleCount);
 
-    for (unsigned sampleIndex(0);sampleIndex<sampleCount;++sampleIndex)
+    for (unsigned sampleIndex(0); sampleIndex<sampleCount; ++sampleIndex)
     {
         _svLoci.getCounts().getSampleCounts(sampleIndex).sampleSource = opt.alignFileOpt.alignmentFilename[sampleIndex];
     }

diff --git a/src/c++/lib/applications/GenerateSVCandidates/SVScorer.cpp b/src/c++/lib/applications/GenerateSVCandidates/SVScorer.cpp
@@ -470,7 +470,7 @@ getSVSupportSummary(
     const unsigned sampleCount(baseInfo.samples.size());
     assert(sampleCount == evidence.samples.size());
 
-    for (unsigned sampleIndex(0);sampleIndex<sampleCount;++sampleIndex)
+    for (unsigned sampleIndex(0); sampleIndex<sampleCount; ++sampleIndex)
     {
         getSampleCounts(evidence.getSampleEvidence(sampleIndex), baseInfo.samples[sampleIndex]);
     }
@@ -592,7 +592,7 @@ resolvePairSplitConflicts(
 
     const unsigned sampleCount(evidence.size());
 
-    for (unsigned sampleIndex(0);sampleIndex<sampleCount;++sampleIndex)
+    for (unsigned sampleIndex(0); sampleIndex<sampleCount; ++sampleIndex)
     {
         resolvePairSplitConflictsSample(isFindAltPairConflict, evidence.getSampleEvidence(sampleIndex));
     }

diff --git a/src/c++/lib/applications/MergeAlignmentStats/MergeAlignmentStatsOptions.hh b/src/c++/lib/applications/MergeAlignmentStats/MergeAlignmentStatsOptions.hh
@@ -36,6 +36,6 @@ struct MergeAlignmentStatsOptions
 
 void
 parseMergeAlignmentStatsOptions(
-        const manta::Program& prog,
-        int argc, char* argv[],
-        MergeAlignmentStatsOptions& opt);
+    const manta::Program& prog,
+    int argc, char* argv[],
+    MergeAlignmentStatsOptions& opt);
diff --git a/src/c++/lib/format/VcfWriterDiploidSV.cpp b/src/c++/lib/format/VcfWriterDiploidSV.cpp
@@ -201,18 +201,18 @@ modifySample(
         const SVScoreInfoDiploidSample& diploidSampleInfo(diploidInfo.samples[diploidSampleIndex]);
 
         values[diploidSampleIndex] =  str( boost::format("%s,%s,%s")
-                         % diploidSampleInfo.phredLoghood[DIPLOID_GT::REF]
-                         % diploidSampleInfo.phredLoghood[DIPLOID_GT::HET]
-                         % diploidSampleInfo.phredLoghood[DIPLOID_GT::HOM]);
+                                           % diploidSampleInfo.phredLoghood[DIPLOID_GT::REF]
+                                           % diploidSampleInfo.phredLoghood[DIPLOID_GT::HET]
+                                           % diploidSampleInfo.phredLoghood[DIPLOID_GT::HOM]);
     }
     sampletags.push_back(std::make_pair("PL",values));
 
     for (unsigned diploidSampleIndex(0); diploidSampleIndex<diploidSampleCount; ++diploidSampleIndex)
     {
         const SVSampleInfo& sampleInfo(baseInfo.samples[diploidSampleIndex]);
         values[diploidSampleIndex] =  str( boost::format("%i,%i")
-                                    % sampleInfo.ref.confidentSpanningPairCount
-                                    % sampleInfo.alt.confidentSpanningPairCount);
+                                           % sampleInfo.ref.confidentSpanningPairCount
+                                           % sampleInfo.alt.confidentSpanningPairCount);
     }
     sampletags.push_back(std::make_pair("PR",values));
 
@@ -222,8 +222,8 @@ modifySample(
     {
         const SVSampleInfo& sampleInfo(baseInfo.samples[diploidSampleIndex]);
         values[diploidSampleIndex] =  str( boost::format("%i,%i")
-                                    % sampleInfo.ref.confidentSplitReadCount
-                                    % sampleInfo.alt.confidentSplitReadCount);
+                                           % sampleInfo.ref.confidentSplitReadCount
+                                           % sampleInfo.alt.confidentSplitReadCount);
     }
     sampletags.push_back(std::make_pair("SR",values));
 
@@ -233,17 +233,17 @@ modifySample(
     {
         const SVSampleInfo& sampleInfo(baseInfo.samples[diploidSampleIndex]);
         values[diploidSampleIndex] =  str( boost::format("%i,%i")
-                                    % sampleInfo.ref.splitReadCount
-                                    % sampleInfo.alt.splitReadCount);
+                                           % sampleInfo.ref.splitReadCount
+                                           % sampleInfo.alt.splitReadCount);
     }
     sampletags.push_back(std::make_pair("FS",values));
 
     for (unsigned diploidSampleIndex(0); diploidSampleIndex<diploidSampleCount; ++diploidSampleIndex)
     {
         const SVSampleInfo& sampleInfo(baseInfo.samples[diploidSampleIndex]);
         values[diploidSampleIndex] =  str( boost::format("%i,%i")
-                                    % sampleInfo.ref.spanningPairCount
-                                    % sampleInfo.alt.spanningPairCount);
+                                           % sampleInfo.ref.spanningPairCount
+                                           % sampleInfo.alt.spanningPairCount);
     }
     sampletags.push_back(std::make_pair("FP",values));
 }

diff --git a/src/c++/lib/manta/SVModelScoreInfo.hh b/src/c++/lib/manta/SVModelScoreInfo.hh
@@ -40,8 +40,8 @@ struct SVModelScoreInfo
         const unsigned sampleCount,
         const unsigned diploidSampleCount)
     {
-      base.setSampleCount(sampleCount);
-      diploid.setSampleCount(diploidSampleCount);
+        base.setSampleCount(sampleCount);
+        diploid.setSampleCount(diploidSampleCount);
     }
 
     void
@@ -57,4 +57,4 @@ struct SVModelScoreInfo
     SVScoreInfoDiploid diploid;
     SVScoreInfoSomatic somatic;
     SVScoreInfoTumor tumor;
-    };
+};
diff --git a/src/c++/lib/svgraph/SVLocusSampleCounts.cpp b/src/c++/lib/svgraph/SVLocusSampleCounts.cpp
@@ -114,7 +114,7 @@ write(
 {
     assert(size() == sampleLabels.size());
     const unsigned s(size());
-    for (unsigned i(0);i<s;++i)
+    for (unsigned i(0); i<s; ++i)
     {
         getSampleCounts(i).write(os,sampleLabels[i].c_str());
     }

diff --git a/src/c++/lib/svgraph/SVLocusSampleCounts.hh b/src/c++/lib/svgraph/SVLocusSampleCounts.hh
@@ -203,7 +203,7 @@ struct AllCounts
         assert(size() == rhs.size());
 
         const unsigned s(size());
-        for (unsigned i(0);i<s;++i)
+        for (unsigned i(0); i<s; ++i)
         {
             getSampleCounts(i).merge(rhs.getSampleCounts(i));
         }

diff --git a/src/c++/lib/svgraph/SVLocusSet.cpp b/src/c++/lib/svgraph/SVLocusSet.cpp
@@ -1048,7 +1048,7 @@ dumpStats(
     {
         std::vector<std::string> labels;
         const unsigned csize(_counts.size());
-        for (unsigned i(0);i<csize;++i)
+        for (unsigned i(0); i<csize; ++i)
         {
             std::ostringstream oss;
             oss << "Sample" << i;

diff --git a/src/python/bin/configManta.py b/src/python/bin/configManta.py
@@ -106,7 +106,7 @@ def validateAndSanitizeExistingOptions(self,options) :
 
 
     def validateOptionExistence(self,options) :
-        
+
         def safeLen(x) :
             if x is None : return 0
             return len(x)

diff --git a/src/python/lib/mantaWorkflow.py b/src/python/lib/mantaWorkflow.py
@@ -110,7 +110,7 @@ def runStats(self,taskPrefix="",dependencies=None) :
 
     nextStepWait = set()
     nextStepWait.add(mergeTask)
-    
+
     rmStatsTmpCmd = "rm -rf " + tmpStatsDir
     rmTask=self.addTask(preJoin(taskPrefix,"rmTmpDir"),rmStatsTmpCmd,dependencies=mergeTask, isForceLocal=True)
 
@@ -160,7 +160,7 @@ def _runDepthShared(self,taskPrefix,dependencies, depthFunc) :
 
     nextStepWait = set()
     nextStepWait.add(mergeTask)
-    
+
     rmTmpCmd = "rm -rf " + tmpDir
     rmTask=self.addTask(preJoin(taskPrefix,"rmTmpDir"),rmTmpCmd,dependencies=mergeTask, isForceLocal=True)
 
@@ -194,22 +194,22 @@ def depthFunc(self,taskPrefix,dependencies,bamFile,outFile) :
 
         tmpDir=os.path.join(outputPath+".tmpdir")
         dirTask=self.addTask(preJoin(taskPrefix,"makeTmpDir"), "mkdir -p "+tmpDir, dependencies=dependencies, isForceLocal=True)
-    
+
         tmpFiles = []
         scatterTasks = set()
-    
+
         for (chromIndex, chromLabel) in enumerate(self.params.chromOrder) :
             cid = getRobustChromId(chromIndex, chromLabel)
             tmpFiles.append(os.path.join(tmpDir,outputFilename+"_"+cid))
             cmd = [self.params.mantaGetChromDepthBin,"--align-file",bamFile,"--chrom",chromLabel,"--output",tmpFiles[-1]]
             scatterTasks.add(self.addTask(preJoin(taskPrefix,"estimateChromDepth_"+cid),cmd,dependencies=dirTask))
-    
+
         catCmd = "cat " + " ".join(["'%s'" % (x) for x in tmpFiles]) + " > '%s'" % (outputPath)
         catTask = self.addTask(preJoin(taskPrefix,"catChromDepth"),catCmd,dependencies=scatterTasks, isForceLocal=True)
-    
+
         nextStepWait = set()
         nextStepWait.add(catTask)
-    
+
         return nextStepWait
 
     return _runDepthShared(self,taskPrefix,dependencies,depthFunc)

diff --git a/src/python/libexec/mergeChromDepth.py b/src/python/libexec/mergeChromDepth.py
@@ -77,10 +77,10 @@ def main() :
             w = line.strip().split('\t')
             assert(w[0] not in chr)
             chr[w[0]] = float(w[1])
-            
+
         if (index!=0) :
             assert(len(chrtot) == len(chr))
-            
+
         for k in chr :
             if (index!=0) :
                 assert(k in chrtot)