Rename 'AS_UTL/' to 'utility/'.

Jolvii85 · Jul 20, 2018 · fb95293 · fb95293
1 parent 15e83fc
commit fb95293
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Showing 141 changed files with 98 additions and 98 deletions.
diff --git a/src/bogart/bogart.mk b/src/bogart/bogart.mk
@@ -34,7 +34,7 @@ SOURCES  := bogart.C \
             AS_BAT_Unitig_AddRead.C \
             AS_BAT_Unitig_PlaceReadUsingEdges.C
 
-SRC_INCDIRS  := .. ../AS_UTL ../stores
+SRC_INCDIRS  := .. ../utility ../stores
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lcanu

diff --git a/src/bogus/bogus.mk b/src/bogus/bogus.mk
@@ -11,7 +11,7 @@ TARGET   := bogus
 SOURCES  := bogus.C \
             bogusUtil.C
 
-SRC_INCDIRS  := .. ../AS_UTL ../stores
+SRC_INCDIRS  := .. ../utility ../stores
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lcanu

diff --git a/src/bogus/bogusness.mk b/src/bogus/bogusness.mk
@@ -10,7 +10,7 @@ endif
 TARGET   := bogusness
 SOURCES  := bogusness.C
 
-SRC_INCDIRS  := .. ../AS_UTL ../stores
+SRC_INCDIRS  := .. ../utility ../stores
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lcanu

diff --git a/src/correction/errorEstimate.mk b/src/correction/errorEstimate.mk
@@ -10,7 +10,7 @@ endif
 TARGET   := errorEstimate
 SOURCES  := errorEstimate.C
 
-SRC_INCDIRS  := .. ../AS_UTL ../stores ../overlapInCore ../utgcns/libNDalign ../overlapErrorAdjustment
+SRC_INCDIRS  := .. ../utility ../stores ../overlapInCore ../utgcns/libNDalign ../overlapErrorAdjustment
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lcanu

diff --git a/src/correction/falconsense.mk b/src/correction/falconsense.mk
@@ -10,7 +10,7 @@ endif
 TARGET   := falconsense
 SOURCES  := falconsense.C ../utgcns/stashContains.C
 
-SRC_INCDIRS  := .. ../AS_UTL ../stores ../utgcns
+SRC_INCDIRS  := .. ../utility ../stores ../utgcns
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lcanu

diff --git a/src/correction/filterCorrectionLayouts.mk b/src/correction/filterCorrectionLayouts.mk
@@ -10,7 +10,7 @@ endif
 TARGET   := filterCorrectionLayouts
 SOURCES  := filterCorrectionLayouts.C
 
-SRC_INCDIRS  := .. ../AS_UTL ../stores
+SRC_INCDIRS  := .. ../utility ../stores
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lcanu

diff --git a/src/correction/filterCorrectionOverlaps.mk b/src/correction/filterCorrectionOverlaps.mk
@@ -10,7 +10,7 @@ endif
 TARGET   := filterCorrectionOverlaps
 SOURCES  := filterCorrectionOverlaps.C
 
-SRC_INCDIRS  := .. ../AS_UTL ../stores
+SRC_INCDIRS  := .. ../utility ../stores
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lcanu

diff --git a/src/correction/generateCorrectionLayouts.mk b/src/correction/generateCorrectionLayouts.mk
@@ -10,7 +10,7 @@ endif
 TARGET   := generateCorrectionLayouts
 SOURCES  := generateCorrectionLayouts.C ../utgcns/stashContains.C
 
-SRC_INCDIRS  := .. ../AS_UTL ../stores ../utgcns
+SRC_INCDIRS  := .. ../utility ../stores ../utgcns
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lcanu

diff --git a/src/correction/readConsensus.mk b/src/correction/readConsensus.mk
@@ -10,7 +10,7 @@ endif
 TARGET   := readConsensus
 SOURCES  := readConsensus.C
 
-SRC_INCDIRS  := .. ../AS_UTL ../stores ../overlapInCore ../utgcns/libNDalign ../overlapErrorAdjustment
+SRC_INCDIRS  := .. ../utility ../stores ../overlapInCore ../utgcns/libNDalign ../overlapErrorAdjustment
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lcanu

diff --git a/src/erateEstimate/erateEstimate.mk b/src/erateEstimate/erateEstimate.mk
@@ -10,7 +10,7 @@ endif
 TARGET   := erateEstimate
 SOURCES  := erateEstimate.C
 
-SRC_INCDIRS  := .. ../AS_UTL ../stores
+SRC_INCDIRS  := .. ../utility ../stores
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lcanu

diff --git a/src/fastq-utilities/fastqAnalyze.mk b/src/fastq-utilities/fastqAnalyze.mk
@@ -10,7 +10,7 @@ endif
 TARGET   := fastqAnalyze
 SOURCES  := fastqAnalyze.C
 
-SRC_INCDIRS  := .. ../AS_UTL
+SRC_INCDIRS  := .. ../utility
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lcanu

diff --git a/src/fastq-utilities/fastqSample.mk b/src/fastq-utilities/fastqSample.mk
@@ -10,7 +10,7 @@ endif
 TARGET   := fastqSample
 SOURCES  := fastqSample.C
 
-SRC_INCDIRS  := .. ../AS_UTL
+SRC_INCDIRS  := .. ../utility
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lcanu

diff --git a/src/fastq-utilities/fastqSimulate-sort.mk b/src/fastq-utilities/fastqSimulate-sort.mk
@@ -10,7 +10,7 @@ endif
 TARGET   := fastqSimulate-sort
 SOURCES  := fastqSimulate-sort.C
 
-SRC_INCDIRS  := .. ../AS_UTL
+SRC_INCDIRS  := .. ../utility
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lcanu

diff --git a/src/fastq-utilities/fastqSimulate.mk b/src/fastq-utilities/fastqSimulate.mk
@@ -10,7 +10,7 @@ endif
 TARGET   := fastqSimulate
 SOURCES  := fastqSimulate.C
 
-SRC_INCDIRS  := .. ../AS_UTL
+SRC_INCDIRS  := .. ../utility
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lcanu

diff --git a/src/gfa/alignGFA.mk b/src/gfa/alignGFA.mk
@@ -10,7 +10,7 @@ endif
 TARGET   := alignGFA
 SOURCES  := alignGFA.C
 
-SRC_INCDIRS  := .. ../AS_UTL ../stores ../overlapInCore/libedlib
+SRC_INCDIRS  := .. ../utility ../stores ../overlapInCore/libedlib
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lcanu

diff --git a/src/haplotyping/splitHaplotype.mk b/src/haplotyping/splitHaplotype.mk
@@ -10,7 +10,7 @@ endif
 TARGET   := splitHaplotype
 SOURCES  := splitHaplotype.C
 
-SRC_INCDIRS  := .. ../AS_UTL ../stores ../utgcns
+SRC_INCDIRS  := .. ../utility ../stores ../utgcns
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lcanu

diff --git a/src/main.mk b/src/main.mk
@@ -26,27 +26,27 @@ TARGET       := libcanu.a
 
 SOURCES      := AS_global.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_alloc.C \
-                \
-                AS_UTL/bitEncodings.C \
-                AS_UTL/bitPackedFile.C \
-                AS_UTL/bitPackedArray.C \
-                AS_UTL/dnaAlphabets.C \
-                AS_UTL/hexDump.C \
-                AS_UTL/md5.C \
-                AS_UTL/memoryMappedFile.C \
-                AS_UTL/mt19937ar.C \
-                AS_UTL/objectStore.C \
-                AS_UTL/readBuffer.C \
-                AS_UTL/speedCounter.C \
-                AS_UTL/sweatShop.C \
-                AS_UTL/timeAndSize.C \
-                AS_UTL/kMer.C \
+                utility/AS_UTL_fasta.C \
+                utility/AS_UTL_fileIO.C \
+                utility/AS_UTL_reverseComplement.C \
+                utility/AS_UTL_stackTrace.C \
+                \
+                utility/AS_UTL_alloc.C \
+                \
+                utility/bitEncodings.C \
+                utility/bitPackedFile.C \
+                utility/bitPackedArray.C \
+                utility/dnaAlphabets.C \
+                utility/hexDump.C \
+                utility/md5.C \
+                utility/memoryMappedFile.C \
+                utility/mt19937ar.C \
+                utility/objectStore.C \
+                utility/readBuffer.C \
+                utility/speedCounter.C \
+                utility/sweatShop.C \
+                utility/timeAndSize.C \
+                utility/kMer.C \
                 \
                 correction/computeGlobalScore.C \
                 correction/falconConsensus.C \
@@ -131,25 +131,25 @@ SOURCES      := AS_global.C \
 
 
 ifeq (${BUILDSTACKTRACE}, 1)
-SOURCES      += AS_UTL/libbacktrace/atomic.c \
-                AS_UTL/libbacktrace/backtrace.c \
-                AS_UTL/libbacktrace/dwarf.c \
-                AS_UTL/libbacktrace/elf.c \
-                AS_UTL/libbacktrace/fileline.c \
-                AS_UTL/libbacktrace/mmap.c \
-                AS_UTL/libbacktrace/mmapio.c \
-                AS_UTL/libbacktrace/posix.c \
-                AS_UTL/libbacktrace/print.c \
-                AS_UTL/libbacktrace/simple.c \
-                AS_UTL/libbacktrace/sort.c \
-                AS_UTL/libbacktrace/state.c \
-                AS_UTL/libbacktrace/unknown.c
+SOURCES      += utility/libbacktrace/atomic.c \
+                utility/libbacktrace/backtrace.c \
+                utility/libbacktrace/dwarf.c \
+                utility/libbacktrace/elf.c \
+                utility/libbacktrace/fileline.c \
+                utility/libbacktrace/mmap.c \
+                utility/libbacktrace/mmapio.c \
+                utility/libbacktrace/posix.c \
+                utility/libbacktrace/print.c \
+                utility/libbacktrace/simple.c \
+                utility/libbacktrace/sort.c \
+                utility/libbacktrace/state.c \
+                utility/libbacktrace/unknown.c
 endif
 
 
 
 SRC_INCDIRS  := . \
-                AS_UTL \
+                utility \
                 stores \
                 stores/libsnappy \
                 alignment \

diff --git a/src/merTrim/merTrim.mk b/src/merTrim/merTrim.mk
@@ -10,7 +10,7 @@ endif
 TARGET   := merTrim
 SOURCES  := merTrim.C
 
-SRC_INCDIRS  := .. ../AS_UTL ../stores ../meryl-san ../meryl-san/libleaff ../meryl-san/libkmer
+SRC_INCDIRS  := .. ../utility ../stores ../meryl-san ../meryl-san/libleaff ../meryl-san/libkmer
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lleaff -lcanu

diff --git a/src/meryl-san/estimate-mer-threshold.mk b/src/meryl-san/estimate-mer-threshold.mk
@@ -11,7 +11,7 @@ endif
 TARGET   := estimate-mer-threshold
 SOURCES  := estimate-mer-threshold.C
 
-SRC_INCDIRS := .. ../AS_UTL libleaff
+SRC_INCDIRS := .. ../utility libleaff
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lleaff -lcanu

diff --git a/src/meryl-san/existDB.mk b/src/meryl-san/existDB.mk
@@ -11,7 +11,7 @@ endif
 TARGET   := existDB
 SOURCES  := existDB.C
 
-SRC_INCDIRS  := .. ../AS_UTL libleaff libkmer
+SRC_INCDIRS  := .. ../utility libleaff libkmer
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lleaff -lcanu

diff --git a/src/meryl-san/leaff.mk b/src/meryl-san/leaff.mk
@@ -17,7 +17,7 @@ SOURCES  := leaff-blocks.C \
             leaff-statistics.C \
             leaff.C
 
-SRC_INCDIRS  := .. ../AS_UTL libleaff
+SRC_INCDIRS  := .. ../utility libleaff
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lleaff -lcanu

diff --git a/src/meryl-san/libleaff.mk b/src/meryl-san/libleaff.mk
@@ -26,7 +26,7 @@ SOURCES  := libleaff/fastaFile.C \
 #            libleaff/test-seqCache.C
 #            libleaff/test-seqStream.C
 
-SRC_INCDIRS  := .. ../AS_UTL ../stores
+SRC_INCDIRS  := .. ../utility ../stores
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := 

diff --git a/src/meryl-san/maskMers.mk b/src/meryl-san/maskMers.mk
@@ -11,7 +11,7 @@ endif
 TARGET   := maskMers
 SOURCES  := maskMers.C
 
-SRC_INCDIRS  := .. ../AS_UTL libleaff
+SRC_INCDIRS  := .. ../utility libleaff
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lleaff -lcanu

diff --git a/src/meryl-san/meryl-san.mk b/src/meryl-san/meryl-san.mk
@@ -18,7 +18,7 @@ SOURCES  := meryl-args.C \
             meryl-unaryOp.C \
             meryl-san.C
 
-SRC_INCDIRS  := .. ../AS_UTL libleaff
+SRC_INCDIRS  := .. ../utility libleaff
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lleaff -lcanu

diff --git a/src/meryl-san/positionDB.mk b/src/meryl-san/positionDB.mk
@@ -11,7 +11,7 @@ endif
 TARGET   := positionDB
 SOURCES  := positionDB.C
 
-SRC_INCDIRS  := .. ../AS_UTL libleaff libkmer
+SRC_INCDIRS  := .. ../utility libleaff libkmer
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lleaff -lcanu

diff --git a/src/meryl-san/simple-dump.mk b/src/meryl-san/simple-dump.mk
@@ -11,7 +11,7 @@ endif
 TARGET   := simple-dump
 SOURCES  := simple-dump.C
 
-SRC_INCDIRS  := .. ../AS_UTL libleaff libkmer
+SRC_INCDIRS  := .. ../utility libleaff libkmer
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lleaff -lcanu

diff --git a/src/meryl-san/simple.mk b/src/meryl-san/simple.mk
@@ -11,7 +11,7 @@ endif
 TARGET   := simple
 SOURCES  := simple.C
 
-SRC_INCDIRS  := .. ../AS_UTL libleaff
+SRC_INCDIRS  := .. ../utility libleaff
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lleaff -lcanu

diff --git a/src/mhap/mhapConvert.mk b/src/mhap/mhapConvert.mk
@@ -10,7 +10,7 @@ endif
 TARGET   := mhapConvert
 SOURCES  := mhapConvert.C
 
-SRC_INCDIRS  := .. ../AS_UTL ../stores liboverlap
+SRC_INCDIRS  := .. ../utility ../stores liboverlap
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lcanu

diff --git a/src/minimap/mmapConvert.mk b/src/minimap/mmapConvert.mk
@@ -10,7 +10,7 @@ endif
 TARGET   := mmapConvert
 SOURCES  := mmapConvert.C
 
-SRC_INCDIRS  := .. ../AS_UTL ../stores liboverlap
+SRC_INCDIRS  := .. ../utility ../stores liboverlap
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lcanu

diff --git a/src/overlapBasedTrimming/splitReads.mk b/src/overlapBasedTrimming/splitReads.mk
@@ -15,7 +15,7 @@ SOURCES  := splitReads.C \
             adjustNormal.C \
             adjustFlipped.C
 
-SRC_INCDIRS  := .. ../AS_UTL ../stores
+SRC_INCDIRS  := .. ../utility ../stores
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lcanu

diff --git a/src/overlapBasedTrimming/trimReads.mk b/src/overlapBasedTrimming/trimReads.mk
@@ -13,7 +13,7 @@ SOURCES  := trimReads.C \
             trimReads-largestCovered.C \
             trimReads-quality.C
 
-SRC_INCDIRS  := .. ../AS_UTL ../stores
+SRC_INCDIRS  := .. ../utility ../stores
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lcanu

diff --git a/src/overlapErrorAdjustment/correctOverlaps.mk b/src/overlapErrorAdjustment/correctOverlaps.mk
@@ -14,7 +14,7 @@ SOURCES  := correctOverlaps.C \
             correctOverlaps-Redo_Olaps.C \
             correctOverlaps-Prefix_Edit_Distance.C
 
-SRC_INCDIRS  := .. ../AS_UTL ../stores ../overlapInCore/liboverlap
+SRC_INCDIRS  := .. ../utility ../stores ../overlapInCore/liboverlap
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lcanu

diff --git a/src/overlapErrorAdjustment/findErrors-Dump.mk b/src/overlapErrorAdjustment/findErrors-Dump.mk
@@ -10,7 +10,7 @@ endif
 TARGET   := findErrors-Dump
 SOURCES  := findErrors-Dump.C
 
-SRC_INCDIRS  := .. ../AS_UTL ../stores ../overlapInCore/liboverlap
+SRC_INCDIRS  := .. ../utility ../stores ../overlapInCore/liboverlap
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lcanu

diff --git a/src/overlapErrorAdjustment/findErrors.mk b/src/overlapErrorAdjustment/findErrors.mk
@@ -16,7 +16,7 @@ SOURCES  := findErrors.C \
             findErrors-Read_Frags.C \
             findErrors-Read_Olaps.C
 
-SRC_INCDIRS  := .. ../AS_UTL ../stores ../overlapInCore/liboverlap
+SRC_INCDIRS  := .. ../utility ../stores ../overlapInCore/liboverlap
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lcanu

diff --git a/src/overlapInCore/edalign.mk b/src/overlapInCore/edalign.mk
@@ -10,7 +10,7 @@ endif
 TARGET   := edalign
 SOURCES  := edalign.C
 
-SRC_INCDIRS  := .. ../AS_UTL ../stores ../meryl/libleaff libedlib
+SRC_INCDIRS  := .. ../utility ../stores ../meryl/libleaff libedlib
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lleaff -lcanu