diff --git a/ChangeLog.txt b/ChangeLog.txt index 749e2bb7..03c6e751 100644 --- a/ChangeLog.txt +++ b/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 diff --git a/src/c++/lib/applications/GenerateSVCandidates/SVFinder.cpp b/src/c++/lib/applications/GenerateSVCandidates/SVFinder.cpp index 9aaa1362..44292a17 100644 --- a/src/c++/lib/applications/GenerateSVCandidates/SVFinder.cpp +++ b/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); diff --git a/src/c++/lib/blt_util/RegionTracker.hh b/src/c++/lib/blt_util/RegionTracker.hh index 0555bee5..0b786ca9 100644 --- a/src/c++/lib/blt_util/RegionTracker.hh +++ b/src/c++/lib/blt_util/RegionTracker.hh @@ -134,7 +134,7 @@ struct RegionPayloadTracker boost::optional isPayloadInRegion( - const pos_t pos) const; + const pos_t pos) const; /// add region /// diff --git a/src/c++/lib/blt_util/RegionTrackerImpl.hh b/src/c++/lib/blt_util/RegionTrackerImpl.hh index 432595af..19b8ae1a 100644 --- a/src/c++/lib/blt_util/RegionTrackerImpl.hh +++ b/src/c++/lib/blt_util/RegionTrackerImpl.hh @@ -23,7 +23,7 @@ template boost::optional RegionPayloadTracker:: isPayloadInRegion( - const pos_t pos) const + const pos_t pos) const { boost::optional result; if (_regions.empty()) return result; @@ -110,7 +110,7 @@ template void RegionPayloadTracker:: removeToPos( - const pos_t pos) + const pos_t pos) { for (auto iter(_regions.begin()) ; iter != _regions.end() ; ++iter) { @@ -125,7 +125,7 @@ template void RegionPayloadTracker:: dump( - std::ostream& os) const + std::ostream& os) const { os << "RegionPayloadTracker\n"; for (const auto& val : _regions) diff --git a/src/cmake/cxxConfigure.cmake b/src/cmake/cxxConfigure.cmake index 9753a72a..fa19c4b1 100644 --- a/src/cmake/cxxConfigure.cmake +++ b/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")