fmt source/update cl

ChangeLog.txt

@@ -1,5 +1,9 @@
+- RNA - parameter adjustments, additional vcf output, orientation fixes
+- MANTA-187 treat split reads symmetrically to improve RNA fusion detection
+-- detect split reads directly rather than via associated soft-clip sequence
+-- exclude split reads from contributing to local assembly evidence
 v0.24.0
--MANTA-213 FFPE runtime optimization:
+- MANTA-213 FFPE runtime optimization:
 -- Recognize new BAM format for fragments shorter than read length,
 prevent these reads from triggering assembly.
 -- Improve insert size distribution estimation by including fragments shorter
@@ -9,7 +13,7 @@ than read length.
 -- Reduce SW edit matrix size with short k-mer match bounds on ref seq
 -- Improve graph noise filtration by testing specific region for evidence
 signal threshold
--- Use adaptive noise rates in hypoth gen step: background read anamoly rate
+-- Use adaptive noise rates in hypoth gen step: background read anomaly rate
 is used to determine if signal is significant. Currently applies to small
 assembly candidates only.
 -- Collapse redundant assembly candidates for small indels to single copy
@@ -32,7 +36,7 @@ v0.22.0
 - MANTA-181 fix assembler path and coverage issues
 - MANTA-177 filter redundant partial insertions
 - MANTA-142 improve contig alignment for large events
-- MANTA-160 add pseudo-coloring to assmembly, and improve multi-pass
+- MANTA-160 add pseudo-coloring to assembly, and improve multi-pass
 read/contig association
 - MANTA-170 improve pair allele support accuracy
 - MANTA-139 add shadow and chimera reads into pair counts
@@ -80,7 +84,7 @@ v0.15.0
 - MANTA-108 combine clip/semi-aligned evidence detection, don't detect
 overlapping reads as assembly evidence
 - MANTA-98 make fewer bam scans during scoring
-- MANTA-106 add high depth limit to candgen and assmbler
+- MANTA-106 add high depth limit to candgen and assembler
 - MANTA-75 Better match reads to SV candidates to improve
 runtime and lower repeat observations (part 2)
 - MANTA-105 filter poorly supported candidates to reduce per-edge compute time

src/c++/lib/applications/GenerateSVCandidates/SVFinder.cpp

@@ -808,7 +808,7 @@ processReadPair(
     for (SVObservation& readCand : _readCandidates)
     {
         using namespace SVEvidenceType;
-        if( readCand.evtype != SPLIT_ALIGN ) continue;
+        if ( readCand.evtype != SPLIT_ALIGN ) continue;
 
         if (readCand.bp1.lowresEvidence.getVal(SPLIT_ALIGN) == 0) readCand.bp1.lowresEvidence.add(SPLIT_ALIGN);
         if (readCand.bp2.lowresEvidence.getVal(SPLIT_ALIGN) == 0) readCand.bp2.lowresEvidence.add(SPLIT_ALIGN);

src/c++/lib/blt_util/RegionTracker.hh

@@ -134,7 +134,7 @@ struct RegionPayloadTracker
 
     boost::optional<T>
     isPayloadInRegion(
-            const pos_t pos) const;
+        const pos_t pos) const;
 
     /// add region
     ///

src/c++/lib/blt_util/RegionTrackerImpl.hh

@@ -23,7 +23,7 @@ template <typename T>
 boost::optional<T>
 RegionPayloadTracker<T>::
 isPayloadInRegion(
-        const pos_t pos) const
+    const pos_t pos) const
 {
     boost::optional<T> result;
     if (_regions.empty()) return result;
@@ -110,7 +110,7 @@ template <typename T>
 void
 RegionPayloadTracker<T>::
 removeToPos(
-        const pos_t pos)
+    const pos_t pos)
 {
     for (auto iter(_regions.begin()) ; iter != _regions.end() ; ++iter)
     {
@@ -125,7 +125,7 @@ template <typename T>
 void
 RegionPayloadTracker<T>::
 dump(
-        std::ostream& os) const
+    std::ostream& os) const
 {
     os << "RegionPayloadTracker\n";
     for (const auto& val : _regions)

src/cmake/cxxConfigure.cmake

@@ -221,7 +221,7 @@ if     (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
     endif ()
 elseif (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
     set (IS_WARN_EVERYTHING FALSE)
-    
+
     if (${IS_WARN_EVERYTHING})
         set (CXX_WARN_FLAGS "${CXX_WARN_FLAGS} -Weverything")
     endif ()
@@ -238,10 +238,10 @@ elseif (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
         set (CXX_WARN_FLAGS "${CXX_WARN_FLAGS} -Wno-c++98-compat -Wno-old-style-cast -Wno-unused-member-function")
         set (CXX_WARN_FLAGS "${CXX_WARN_FLAGS} -Wno-documentation -Wno-float-equal")
     endif ()
-    
+
     if (NOT (${compiler_version} VERSION_LESS "3.3"))
         set (CXX_WARN_FLAGS "${CXX_WARN_FLAGS} -Woverloaded-shift-op-parentheses")
-        
+
         if (${IS_WARN_EVERYTHING})
             set (CXX_WARN_FLAGS "${CXX_WARN_FLAGS} -Wno-documentation-unknown-command")
         endif ()
@@ -264,7 +264,7 @@ elseif (CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
     set (CXX_WARN_FLAGS "${CXX_WARN_FLAGS} -diag-disable 177,193,869,1599,3280")
 
     set (CXX_WARN_FLAGS "${CXX_WARN_FLAGS} -Wunused-variable -Wpointer-arith")
-    
+
     #set (CXX_WARN_FLAGS "${CXX_WARN_FLAGS} -Wmissing-prototypes -Wmissing-declarations -Wunused-variable -Wpointer-arith -Wuninitialized")
 endif()
 
@@ -277,12 +277,12 @@ if (GNU_COMPAT_COMPILER)
     set (CMAKE_CXX_FLAGS_DEBUG "-O0 -g")
 
     # The NDEBUG macro is intentionally removed from release. One discussion on this is:
-    # http://www.drdobbs.com/an-exception-or-a-bug/184401686    
+    # http://www.drdobbs.com/an-exception-or-a-bug/184401686
     set (CMAKE_CXX_FLAGS_RELEASE "-O3 -fomit-frame-pointer")
     set (CMAKE_CXX_FLAGS_RELWITHDEBINFO "-O2 -g")
     set (CMAKE_CXX_FLAGS_ASAN "-O1 -g -fsanitize=address -fno-omit-frame-pointer -fno-optimize-sibling-calls")
     #set (CMAKE_CXX_FLAGS_PROFILE "-O0 -g -pg -fprofile-arcs -ftest-coverage")
-    
+
     # this doesn't seem to impact performance, taking out for now:
     #if (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
     #    set (CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -flto")