From 53de6aeb0f2f27a9ebd138439f8903e623014533 Mon Sep 17 00:00:00 2001 From: "Brian P. Walenz" Date: Tue, 18 Aug 2015 19:40:31 +0000 Subject: [PATCH] Tidy up main.mk, remove several unused main.mk from subdirectories. --- src/AS_UTL/main.mk | 47 ------- src/bogart/main.mk | 1 - src/bogus/main.mk | 20 --- src/erateEstimate/main.mk | 1 - src/fastq-utilities/main.mk | 22 --- src/main.mk | 268 +++++++++++++++++------------------- src/overlapInCore/main.mk | 1 - src/stores/main.mk | 30 ---- 8 files changed, 130 insertions(+), 260 deletions(-) delete mode 100644 src/AS_UTL/main.mk delete mode 120000 src/bogart/main.mk delete mode 100644 src/bogus/main.mk delete mode 120000 src/erateEstimate/main.mk delete mode 100644 src/fastq-utilities/main.mk delete mode 120000 src/overlapInCore/main.mk delete mode 100644 src/stores/main.mk diff --git a/src/AS_UTL/main.mk b/src/AS_UTL/main.mk deleted file mode 100644 index 22b8dc4ba..000000000 --- a/src/AS_UTL/main.mk +++ /dev/null @@ -1,47 +0,0 @@ - -# 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)-$(MACHINETYPE)/bin -endif - -TARGET := libCA.a - -SOURCES := AS_UTL_GPL.C \ - AS_UTL_Hash.C \ - AS_UTL_Var.C \ - AS_UTL_alloc.C \ - AS_UTL_decodeRange.C \ - AS_UTL_fasta.C \ - AS_UTL_fileIO.C \ - AS_UTL_heap.C \ - AS_UTL_histo.C \ - AS_UTL_interval.C \ - AS_UTL_rand.C \ - AS_UTL_reverseComplement.C \ - AS_UTL_stackTrace.C \ - bitEncodings.C \ - bitPackedFile.C \ - bitPackedArray.C \ - dnaAlphabets.C \ - md5.C \ - mt19937ar.C \ - readBuffer.C \ - speedCounter.C \ - sweatShop.C \ - timeAndSize.C \ - kMer.C - -# decodeBooleanString.C \ -# AS_UTL_stackTraceTest.C \ -# AS_UTL_testhisto.C \ -# memoryMappedFileTest.C \ -# testHashTable.C \ -# testRand.C \ -# testVar.C \ - -SRC_INCDIRS := . .. -SUBMAKEFILES := diff --git a/src/bogart/main.mk b/src/bogart/main.mk deleted file mode 120000 index 3d6589113..000000000 --- a/src/bogart/main.mk +++ /dev/null @@ -1 +0,0 @@ -bogart.mk \ No newline at end of file diff --git a/src/bogus/main.mk b/src/bogus/main.mk deleted file mode 100644 index d2025215c..000000000 --- a/src/bogus/main.mk +++ /dev/null @@ -1,20 +0,0 @@ -# If 'make' isn't run from the root directory, we need to set these to -# point to the upper level build directory. -ifeq "$(strip ${BUILD_DIR})" "" - BUILD_DIR := ../$(OSTYPE)-$(MACHINETYPE)/obj -endif -ifeq "$(strip ${TARGET_DIR})" "" - TARGET_DIR := ../$(OSTYPE)-$(MACHINETYPE)/bin -endif - -TARGET := libCA.a -SOURCES := bogusUtil.C - -SRC_INCDIRS := .. ../AS_UTL ../stores - -TGT_LDFLAGS := -L${TARGET_DIR} -TGT_LDLIBS := -lCA -TGT_PREREQS := libCA.a - -SUBMAKEFILES := bogus.mk \ - bogusness.mk diff --git a/src/erateEstimate/main.mk b/src/erateEstimate/main.mk deleted file mode 120000 index 125c17d35..000000000 --- a/src/erateEstimate/main.mk +++ /dev/null @@ -1 +0,0 @@ -erateEstimate.mk \ No newline at end of file diff --git a/src/fastq-utilities/main.mk b/src/fastq-utilities/main.mk deleted file mode 100644 index 53a07fef3..000000000 --- a/src/fastq-utilities/main.mk +++ /dev/null @@ -1,22 +0,0 @@ -# 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)-$(MACHINETYPE)/bin -endif - -TARGET := -SOURCES := - -SRC_INCDIRS := .. ../AS_UTL ../stores - -TGT_LDFLAGS := -L${TARGET_DIR} -TGT_LDLIBS := -lCA -TGT_PREREQS := libCA.a - -SUBMAKEFILES := fastqAnalyze.mk \ - fastqSample.mk \ - fastqSimulate.mk \ - fastqSimulate-sort.mk diff --git a/src/main.mk b/src/main.mk index c565b671e..f72059d18 100644 --- a/src/main.mk +++ b/src/main.mk @@ -8,147 +8,139 @@ ifeq "$(strip ${TARGET_DIR})" "" TARGET_DIR := ../$(OSTYPE)-$(MACHINETYPE)/bin endif -TARGET := libCA.a +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 \ - \ - 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 +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 \ + \ + 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 -SRC_INCDIRS := . AS_UTL stores alignment utgcns/libNDalign utgcns/libcns meryl/libleaff overlapInCore overlapInCore/liboverlap +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 \ diff --git a/src/overlapInCore/main.mk b/src/overlapInCore/main.mk deleted file mode 120000 index e0fe40ee1..000000000 --- a/src/overlapInCore/main.mk +++ /dev/null @@ -1 +0,0 @@ -overlapInCore.mk \ No newline at end of file diff --git a/src/stores/main.mk b/src/stores/main.mk deleted file mode 100644 index 50e02d819..000000000 --- a/src/stores/main.mk +++ /dev/null @@ -1,30 +0,0 @@ -# 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 - -SOURCES := gkStore.C \ - ovOverlap.C \ - ovStore.C \ - ovStoreFile.C \ - tgStore.C \ - tgTig.C - -SRC_INCDIRS := .. ../AS_UTL -SUBMAKEFILES := gatekeeperCreate.mk \ - gatekeeperDumpFASTQ.mk \ - gatekeeperDumpMetaData.mk \ - gatekeeperPartition.mk \ - ovStoreBuild.mk \ - ovStoreBucketizer.mk \ - ovStoreSorter.mk \ - ovStoreIndexer.mk \ - ovStoreDump.mk \ - tgStoreDump.mk \ - tgTigDisplay.mk