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main.mk
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MODULE := canu
TARGET := libcanu.a
SOURCES := utility/src/align/align-ksw2-driver.C \
utility/src/align/align-ksw2-extz.C \
utility/src/align/align-ksw2-extz2-sse.C \
utility/src/align/align-parasail-driver.C \
utility/src/align/align-ssw-driver.C \
utility/src/align/align-ssw.C \
utility/src/align/edlib.C \
\
utility/src/bits/fibonacci-v1.C \
utility/src/bits/hexDump-v1.C \
utility/src/bits/stuffedBits-v1-binary.C \
utility/src/bits/stuffedBits-v1-bits.C \
utility/src/bits/stuffedBits-v1-delta.C \
utility/src/bits/stuffedBits-v1-gamma.C \
utility/src/bits/stuffedBits-v1-golomb.C \
utility/src/bits/stuffedBits-v1-omega.C \
utility/src/bits/stuffedBits-v1-unary.C \
utility/src/bits/stuffedBits-v1-zeckendorf.C \
utility/src/bits/stuffedBits-v1.C \
utility/src/bits/wordArray-v1.C \
\
utility/src/datastructures/keyAndValue-v1.C \
utility/src/datastructures/splitToWords-v1.C \
utility/src/datastructures/stringList-v1.C \
utility/src/datastructures/strings-v1.C \
utility/src/datastructures/types-v1.C \
\
utility/src/files/accessing-v1.C \
utility/src/files/buffered-v1-reading.C \
utility/src/files/buffered-v1-writing.C \
utility/src/files/compressed-v1-reading.C \
utility/src/files/compressed-v1-writing.C \
utility/src/files/compressed-v1.C \
utility/src/files/fasta-fastq-v1.C \
utility/src/files/files-v1.C \
utility/src/files/memoryMapped-v1.C \
utility/src/files/readLine-v0.C \
utility/src/files/readLine-v1.C \
utility/src/files/reading-v1.C \
utility/src/files/writing-v1.C \
\
utility/src/kmers-v1/kmers-exact.C \
utility/src/kmers-v1/kmers-files.C \
utility/src/kmers-v1/kmers-histogram.C \
utility/src/kmers-v1/kmers-reader.C \
utility/src/kmers-v1/kmers-writer-block.C \
utility/src/kmers-v1/kmers-writer-stream.C \
utility/src/kmers-v1/kmers-writer.C \
utility/src/kmers-v1/kmers.C \
\
utility/src/kmers-v2/kmers-exact.C \
utility/src/kmers-v2/kmers-files.C \
utility/src/kmers-v2/kmers-histogram.C \
utility/src/kmers-v2/kmers-reader-dump.C \
utility/src/kmers-v2/kmers-reader.C \
utility/src/kmers-v2/kmers-writer-block.C \
utility/src/kmers-v2/kmers-writer-stream.C \
utility/src/kmers-v2/kmers-writer.C \
utility/src/kmers-v2/kmers.C \
\
utility/src/math/md5-v1.C \
utility/src/math/mt19937ar-v1.C \
utility/src/math/sampledDistribution-v1.C \
\
utility/src/parasail/cpuid.c \
utility/src/parasail/cigar.c \
utility/src/parasail/memory.c \
utility/src/parasail/sg.c \
utility/src/parasail/sg_trace.c \
utility/src/parasail/sg_qb_de_dispatch.c \
utility/src/parasail/sg_qe_db_dispatch.c \
utility/src/parasail/sg_qx_dispatch.c \
utility/src/parasail/sg_trace.c \
\
utility/src/sequence/dnaSeq-v1.C \
utility/src/sequence/dnaSeqFile-v1.C \
utility/src/sequence/sequence-v1.C \
\
utility/src/system/logging-v1.C \
utility/src/system/runtime-v1.C \
utility/src/system/speedCounter-v1.C \
utility/src/system/sweatShop-v1.C \
utility/src/system/system-stackTrace-v1.C \
utility/src/system/system-v1.C \
utility/src/system/time-v1.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 \
\
gfa/gfa.C \
gfa/bed.C
ifeq (${BUILDSTACKTRACE}, 1)
SOURCES += utility/src/system/libbacktrace/atomic.c \
utility/src/system/libbacktrace/backtrace.c \
utility/src/system/libbacktrace/dwarf.c \
utility/src/system/libbacktrace/elf.c \
utility/src/system/libbacktrace/fileline.c \
utility/src/system/libbacktrace/mmap.c \
utility/src/system/libbacktrace/mmapio.c \
utility/src/system/libbacktrace/posix.c \
utility/src/system/libbacktrace/print.c \
utility/src/system/libbacktrace/simple.c \
utility/src/system/libbacktrace/sort.c \
utility/src/system/libbacktrace/state.c \
utility/src/system/libbacktrace/unknown.c
endif
SRC_INCDIRS := utility/src \
stores \
stores/libsnappy \
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 \
\
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 \
\
utgcns/utgcns.mk \
utgcns/layoutToPackage.mk \
\
gfa/alignGFA.mk
EXECUTABLES := pipelines/canu.pl -> bin/canu \
pipelines/canu-time.pl -> bin/canu-time \
pipelines/draw-tig.pl -> bin/draw-tig
FILES += pipelines/canu.defaults -> bin/canu.defaults \
mhap/mhap-2.1.3.jar -> share/java/classes/mhap-2.1.3.jar \
pipelines/canu/Consensus.pm -> lib/site_perl/canu/Consensus.pm \
pipelines/canu/CorrectReads.pm -> lib/site_perl/canu/CorrectReads.pm \
pipelines/canu/HaplotypeReads.pm -> lib/site_perl/canu/HaplotypeReads.pm \
pipelines/canu/Configure.pm -> lib/site_perl/canu/Configure.pm \
pipelines/canu/Defaults.pm -> lib/site_perl/canu/Defaults.pm \
pipelines/canu/Execution.pm -> lib/site_perl/canu/Execution.pm \
pipelines/canu/SequenceStore.pm -> lib/site_perl/canu/SequenceStore.pm \
pipelines/canu/Grid.pm -> lib/site_perl/canu/Grid.pm \
pipelines/canu/Grid_Cloud.pm -> lib/site_perl/canu/Grid_Cloud.pm \
pipelines/canu/Grid_DNANexus.pm -> lib/site_perl/canu/Grid_DNANexus.pm \
pipelines/canu/Grid_LSF.pm -> lib/site_perl/canu/Grid_LSF.pm \
pipelines/canu/Grid_Local.pm -> lib/site_perl/canu/Grid_Local.pm \
pipelines/canu/Grid_PBSTorque.pm -> lib/site_perl/canu/Grid_PBSTorque.pm \
pipelines/canu/Grid_SGE.pm -> lib/site_perl/canu/Grid_SGE.pm \
pipelines/canu/Grid_Slurm.pm -> lib/site_perl/canu/Grid_Slurm.pm \
pipelines/canu/Meryl.pm -> lib/site_perl/canu/Meryl.pm \
pipelines/canu/Output.pm -> lib/site_perl/canu/Output.pm \
pipelines/canu/OverlapBasedTrimming.pm -> lib/site_perl/canu/OverlapBasedTrimming.pm \
pipelines/canu/OverlapErrorAdjustment.pm -> lib/site_perl/canu/OverlapErrorAdjustment.pm \
pipelines/canu/OverlapInCore.pm -> lib/site_perl/canu/OverlapInCore.pm \
pipelines/canu/OverlapMhap.pm -> lib/site_perl/canu/OverlapMhap.pm \
pipelines/canu/OverlapMMap.pm -> lib/site_perl/canu/OverlapMMap.pm \
pipelines/canu/OverlapStore.pm -> lib/site_perl/canu/OverlapStore.pm \
pipelines/canu/Report.pm -> lib/site_perl/canu/Report.pm \
pipelines/canu/Unitig.pm -> lib/site_perl/canu/Unitig.pm