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main.mk
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main.mk
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MODULE := canu
TARGET := libcanu.a
SOURCES := utility/src/utility/runtime.C \
\
utility/src/utility/align-ssw.C \
utility/src/utility/align-ssw-driver.C \
utility/src/utility/edlib.C \
\
utility/src/utility/files.C \
utility/src/utility/files-buffered.C \
utility/src/utility/files-compressed.C \
utility/src/utility/files-memoryMapped.C \
\
utility/src/utility/logging.C \
\
utility/src/utility/strings.C \
\
utility/src/utility/system.C \
utility/src/utility/system-stackTrace.C \
\
utility/src/utility/sequence.C \
\
utility/src/utility/types.C \
\
utility/src/utility/kmers-exact.C \
utility/src/utility/kmers-files.C \
utility/src/utility/kmers-histogram.C \
utility/src/utility/kmers-reader.C \
utility/src/utility/kmers-writer-block.C \
utility/src/utility/kmers-writer-stream.C \
utility/src/utility/kmers-writer.C \
utility/src/utility/kmers.C \
\
utility/src/utility/bits.C \
\
utility/src/utility/hexDump.C \
utility/src/utility/md5.C \
utility/src/utility/mt19937ar.C \
utility/src/utility/speedCounter.C \
utility/src/utility/sweatShop.C \
\
correction/computeGlobalScore.C \
correction/falconConsensus.C \
correction/falconConsensus-alignTag.C \
\
stores/sqCache.C \
stores/sqLibrary.C \
stores/sqReadData.C \
stores/sqReadDataWriter.C \
stores/sqStore.C \
stores/sqStoreBlob.C \
stores/sqStoreConstructor.C \
stores/sqStoreInfo.C \
\
stores/ovOverlap.C \
stores/ovStore.C \
stores/ovStoreWriter.C \
stores/ovStoreFilter.C \
stores/ovStoreFile.C \
stores/ovStoreHistogram.C \
\
stores/tgStore.C \
stores/tgTig.C \
stores/tgTigSizeAnalysis.C \
stores/tgTigMultiAlignDisplay.C \
\
stores/libsnappy/snappy-sinksource.cc \
stores/libsnappy/snappy-stubs-internal.cc \
stores/libsnappy/snappy.cc \
\
stores/objectStore.C \
\
overlapInCore/overlapReadCache.C \
\
overlapInCore/liboverlap/Binomial_Bound.C \
overlapInCore/liboverlap/Display_Alignment.C \
overlapInCore/liboverlap/prefixEditDistance.C \
overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.C \
overlapInCore/liboverlap/prefixEditDistance-extend.C \
overlapInCore/liboverlap/prefixEditDistance-forward.C \
overlapInCore/liboverlap/prefixEditDistance-reverse.C \
\
utgcns/libNDalign/NDalign.C \
\
utgcns/libNDalign/Binomial_Bound.C \
utgcns/libNDalign/NDalgorithm.C \
utgcns/libNDalign/NDalgorithm-allocateMoreSpace.C \
utgcns/libNDalign/NDalgorithm-extend.C \
utgcns/libNDalign/NDalgorithm-forward.C \
utgcns/libNDalign/NDalgorithm-reverse.C \
\
utgcns/libpbutgcns/AlnGraphBoost.C \
\
gfa/gfa.C \
gfa/bed.C
ifeq (${BUILDSTACKTRACE}, 1)
SOURCES += utility/src/utility/libbacktrace/atomic.c \
utility/src/utility/libbacktrace/backtrace.c \
utility/src/utility/libbacktrace/dwarf.c \
utility/src/utility/libbacktrace/elf.c \
utility/src/utility/libbacktrace/fileline.c \
utility/src/utility/libbacktrace/mmap.c \
utility/src/utility/libbacktrace/mmapio.c \
utility/src/utility/libbacktrace/posix.c \
utility/src/utility/libbacktrace/print.c \
utility/src/utility/libbacktrace/simple.c \
utility/src/utility/libbacktrace/sort.c \
utility/src/utility/libbacktrace/state.c \
utility/src/utility/libbacktrace/unknown.c
endif
SRC_INCDIRS := . \
utility/src/utility \
stores \
stores/libsnappy \
alignment \
utgcns/libNDalign \
utgcns/libcns \
utgcns/libpbutgcns \
utgcns/libNDFalcon \
utgcns/libboost \
overlapInCore \
overlapInCore/liboverlap
SUBMAKEFILES := stores/dumpBlob.mk \
stores/ovStoreBuild.mk \
stores/ovStoreConfig.mk \
stores/ovStoreBucketizer.mk \
stores/ovStoreSorter.mk \
stores/ovStoreIndexer.mk \
stores/ovStoreDump.mk \
stores/ovStoreStats.mk \
stores/sqStoreCreate.mk \
stores/sqStoreDumpFASTQ.mk \
stores/sqStoreDumpMetaData.mk \
stores/tgStoreCompress.mk \
stores/tgStoreDump.mk \
stores/tgStoreLoad.mk \
stores/tgTigDisplay.mk \
stores/loadCorrectedReads.mk \
stores/loadTrimmedReads.mk \
stores/loadErates.mk \
\
meryl/src/meryl/meryl.mk \
\
overlapInCore/overlapInCore.mk \
overlapInCore/overlapInCorePartition.mk \
overlapInCore/overlapConvert.mk \
overlapInCore/overlapImport.mk \
overlapInCore/overlapPair.mk \
overlapInCore/edalign.mk \
\
overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.mk \
\
mhap/mhapConvert.mk \
\
minimap/mmapConvert.mk \
\
correction/filterCorrectionOverlaps.mk \
correction/generateCorrectionLayouts.mk \
correction/filterCorrectionLayouts.mk \
correction/falconsense.mk \
\
correction/errorEstimate.mk \
\
haplotyping/splitHaplotype.mk \
\
overlapBasedTrimming/trimReads.mk \
overlapBasedTrimming/splitReads.mk \
overlapBasedTrimming/mergeRanges.mk \
\
overlapAlign/overlapAlign.mk \
\
overlapErrorAdjustment/findErrors.mk \
overlapErrorAdjustment/fixErrors.mk \
overlapErrorAdjustment/findErrors-Dump.mk \
overlapErrorAdjustment/correctOverlaps.mk \
\
bogart/bogart.mk \
bogart/layoutReads.mk \
\
bogus/bogus.mk \
\
utgcns/utgcns.mk \
\
gfa/alignGFA.mk