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main.mk
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# If 'make' isn't run from the root directory, we need to set these to
# point to the upper level build directory.
ifeq "$(strip ${BUILD_DIR})" ""
BUILD_DIR := ../$(OSTYPE)-$(MACHINETYPE)/obj
endif
ifeq "$(strip ${TARGET_DIR})" ""
TARGET_DIR := ../$(OSTYPE)-$(MACHINETYPE)/bin
endif
TARGET := libCA.a
# unitigger uses AS_UTL_alloc, AS_UTL_Var and AS_UTL_Hash
# AS_UTL_Hash needs AS_UTL_heap
SOURCES := AS_global.C \
\
AS_UTL/AS_UTL_decodeRange.C \
AS_UTL/AS_UTL_fasta.C \
AS_UTL/AS_UTL_fileIO.C \
AS_UTL/AS_UTL_reverseComplement.C \
AS_UTL/AS_UTL_stackTrace.C \
\
AS_UTL/AS_UTL_Var.C \
AS_UTL/AS_UTL_Hash.C \
AS_UTL/AS_UTL_heap.C \
AS_UTL/AS_UTL_alloc.C \
\
AS_UTL/bitEncodings.C \
AS_UTL/bitPackedFile.C \
AS_UTL/bitPackedArray.C \
AS_UTL/dnaAlphabets.C \
AS_UTL/md5.C \
AS_UTL/mt19937ar.C \
AS_UTL/readBuffer.C \
AS_UTL/speedCounter.C \
AS_UTL/stddev.C \
AS_UTL/sweatShop.C \
AS_UTL/timeAndSize.C \
AS_UTL/kMer.C \
\
stores/gkStore.C \
\
stores/ovOverlap.C \
stores/ovStore.C \
stores/ovStoreFile.C \
\
stores/tgStore.C \
stores/tgTig.C \
stores/tgTigSizeAnalysis.C \
stores/tgTigMultiAlignDisplay.C \
\
meryl/libmeryl.C \
\
alignment/alignment-drivers.C \
alignment/analyze-affine-overlap.C \
alignment/brute-force-dp.C \
alignment/dp-align.C \
alignment/find-local-overlap.C \
alignment/find-local-segments.C \
alignment/fix-overlapping-pieces.C \
alignment/local-overlapper.C \
\
overlapInCore/overlapReadCache.C \
\
\
overlapErrorAdjustment/analyzeAlignment.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 \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-5000.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-4900.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-4800.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-4700.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-4600.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-4500.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-4400.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-4300.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-4200.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-4100.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-4000.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-3900.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-3800.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-3700.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-3600.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-3500.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-3400.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-3300.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-3200.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-3100.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-3000.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-2900.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-2800.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-2700.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-2600.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-2500.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-2400.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-2300.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-2200.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-2100.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-2000.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-1900.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-1800.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-1700.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-1600.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-1500.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-1400.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-1300.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-1200.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-1100.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-1000.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-0900.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-0800.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-0700.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-0600.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-0500.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-0400.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-0300.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-0200.C \
overlapInCore/liboverlap/prefixEditDistance-matchLimit-0100.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/libcns/abAbacus-addRead.C \
utgcns/libcns/abAbacus-applyAlignment.C \
utgcns/libcns/abAbacus-baseCall.C \
utgcns/libcns/abAbacus-mergeRefine.C \
utgcns/libcns/abAbacus-refine.C \
utgcns/libcns/abAbacus-refreshMultiAlign.C \
utgcns/libcns/abAbacus.C \
utgcns/libcns/abColumn.C \
utgcns/libcns/abMultiAlign.C \
utgcns/libcns/unitigConsensus.C
# Not complete, just snippets of code
# AS_UTL/decodeBooleanString.C
# AS_UTL/AS_UTL_stackTraceTest.C
#
# Test code
# AS_UTL/testHashTable.C
# AS_UTL/testRand.C
# AS_UTL/testVar.C
# AS_UTL/memoryMappedFileTest.C
SRC_INCDIRS := . AS_UTL stores alignment utgcns/libNDalign utgcns/libcns meryl/libleaff overlapInCore overlapInCore/liboverlap
# Cannot be the 'main.mk' from subdirectories, as that redefines libCA.a to
# update just those objects. Instead, this must list each binary indifidually.
SUBMAKEFILES := stores/gatekeeperCreate.mk \
stores/gatekeeperDumpFASTQ.mk \
stores/gatekeeperDumpMetaData.mk \
stores/gatekeeperPartition.mk \
stores/ovStoreBuild.mk \
stores/ovStoreBucketizer.mk \
stores/ovStoreSorter.mk \
stores/ovStoreIndexer.mk \
stores/ovStoreDump.mk \
stores/tgStoreDump.mk \
stores/tgTigDisplay.mk \
\
meryl/libleaff.mk \
meryl/leaff.mk \
meryl/meryl.mk \
meryl/simple.mk \
meryl/estimate-mer-threshold.mk \
\
overlapInCore/overlapInCore.mk \
overlapInCore/overlapInCorePartition.mk \
overlapInCore/overlapConvert.mk \
overlapInCore/overlapImport.mk \
overlapInCore/overlapPair.mk \
\
overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.mk \
\
mhap/mhap.mk \
mhap/mhapConvert.mk \
\
correction/filterCorrectionOverlaps.mk \
correction/generateCorrectionLayouts.mk \
correction/readConsensus.mk \
\
falcon_sense/createFalconSenseInputs.mk \
\
overlapBasedTrimming/trimReads.mk \
overlapBasedTrimming/splitReads.mk \
\
overlapErrorAdjustment/findErrors.mk \
overlapErrorAdjustment/correctOverlaps.mk \
\
bogart/bogart.mk \
\
bogus/bogus.mk \
\
erateEstimate/erateEstimate.mk \
\
unitigger/unitigger.mk \
\
utgcns/utgcns.mk \
\
fastq-utilities/fastqAnalyze.mk \
fastq-utilities/fastqSample.mk \
fastq-utilities/fastqSimulate.mk \
fastq-utilities/fastqSimulate-sort.mk