Move various bits used only by meryl et alia from utility/ to meryl-s…

…an/.

src/main.mk

@@ -32,10 +32,6 @@ SOURCES      := AS_global.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 \
@@ -45,7 +41,6 @@ SOURCES      := AS_global.C \
                 utility/speedCounter.C \
                 utility/sweatShop.C \
                 utility/timeAndSize.C \
-                utility/kMer.C \
                 \
                 correction/computeGlobalScore.C \
                 correction/falconConsensus.C \
@@ -74,8 +69,6 @@ SOURCES      := AS_global.C \
                 stores/libsnappy/snappy-stubs-internal.cc \
                 stores/libsnappy/snappy.cc \
                 \
-                meryl-san/libmeryl-san.C \
-                \
                 overlapInCore/overlapReadCache.C \
                 \
                 overlapErrorAdjustment/analyzeAlignment.C \
@@ -115,17 +108,6 @@ SOURCES      := AS_global.C \
                 gfa/gfa.C \
                 gfa/bed.C \
                 \
-                meryl-san/libkmer/existDB-create-from-fasta.C \
-                meryl-san/libkmer/existDB-create-from-meryl.C \
-                meryl-san/libkmer/existDB-create-from-sequence.C \
-                meryl-san/libkmer/existDB-state.C \
-                meryl-san/libkmer/existDB.C \
-                meryl-san/libkmer/positionDB-access.C \
-                meryl-san/libkmer/positionDB-dump.C \
-                meryl-san/libkmer/positionDB-file.C \
-                meryl-san/libkmer/positionDB-mismatch.C \
-                meryl-san/libkmer/positionDB-sort.C \
-                meryl-san/libkmer/positionDB.C
 
 
 
@@ -157,7 +139,6 @@ SRC_INCDIRS  := . \
                 utgcns/libpbutgcns \
                 utgcns/libNDFalcon \
                 utgcns/libboost \
-                meryl-san/libleaff \
                 overlapInCore \
                 overlapInCore/libedlib \
                 overlapInCore/liboverlap
@@ -194,7 +175,6 @@ SUBMAKEFILES := stores/dumpBlob.mk \
                 meryl-san/positionDB.mk \
                 meryl-san/simple-dump.mk \
                 \
-                merTrim/merTrim.mk \
                 \
                 overlapInCore/overlapInCore.mk \
                 overlapInCore/overlapInCorePartition.mk \

src/meryl-san/estimate-mer-threshold.mk

@@ -11,7 +11,7 @@ endif
 TARGET   := estimate-mer-threshold
 SOURCES  := estimate-mer-threshold.C
 
-SRC_INCDIRS := .. ../utility libleaff
+SRC_INCDIRS := . ./libleaff ./utility ./libkmer .. ../utility libleaff
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lleaff -lcanu

src/meryl-san/existDB.mk

@@ -11,7 +11,7 @@ endif
 TARGET   := existDB
 SOURCES  := existDB.C
 
-SRC_INCDIRS  := .. ../utility libleaff libkmer
+SRC_INCDIRS  := . ./libleaff ./utility ./libkmer .. ../utility libleaff libkmer
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lleaff -lcanu

src/meryl-san/leaff.mk

@@ -17,7 +17,7 @@ SOURCES  := leaff-blocks.C \
             leaff-statistics.C \
             leaff.C
 
-SRC_INCDIRS  := .. ../utility libleaff
+SRC_INCDIRS  := . ./libleaff ./utility ./libkmer .. ../utility libleaff
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lleaff -lcanu

src/meryl-san/libleaff.mk

@@ -9,7 +9,8 @@ ifeq "$(strip ${TARGET_DIR})" ""
 endif
 
 TARGET   := libleaff.a
-SOURCES  := libleaff/fastaFile.C \
+SOURCES  := libleaff/dnaAlphabets.C \
+            libleaff/fastaFile.C \
             libleaff/fastaStdin.C \
             libleaff/fastqFile.C \
             libleaff/fastqStdin.C \
@@ -19,14 +20,30 @@ SOURCES  := libleaff/fastaFile.C \
             libleaff/seqFactory.C \
             libleaff/seqStore.C \
             libleaff/seqStream.C \
-            libleaff/sffFile.C
+            libleaff/sffFile.C \
+            utility/bitEncodings.C \
+            utility/bitPackedFile.C \
+            utility/bitPackedArray.C \
+            utility/kMer.C \
+            libkmer/existDB-create-from-fasta.C \
+            libkmer/existDB-create-from-meryl.C \
+            libkmer/existDB-create-from-sequence.C \
+            libkmer/existDB-state.C \
+            libkmer/existDB.C \
+            libkmer/positionDB-access.C \
+            libkmer/positionDB-dump.C \
+            libkmer/positionDB-file.C \
+            libkmer/positionDB-mismatch.C \
+            libkmer/positionDB-sort.C \
+            libkmer/positionDB.C \
+            libmeryl-san.C
 
 #            libleaff/selftest.C
 #            libleaff/test-merStream.C
 #            libleaff/test-seqCache.C
 #            libleaff/test-seqStream.C
 
-SRC_INCDIRS  := .. ../utility ../stores
+SRC_INCDIRS  := . ./libleaff ./utility ./libkmer .. ../utility ../stores
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := 

src/meryl-san/maskMers.mk

@@ -11,7 +11,7 @@ endif
 TARGET   := maskMers
 SOURCES  := maskMers.C
 
-SRC_INCDIRS  := .. ../utility libleaff
+SRC_INCDIRS  := . ./libleaff ./utility ./libkmer .. ../utility libleaff
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lleaff -lcanu

src/meryl-san/meryl-san.mk

@@ -18,7 +18,7 @@ SOURCES  := meryl-args.C \
             meryl-unaryOp.C \
             meryl-san.C
 
-SRC_INCDIRS  := .. ../utility libleaff
+SRC_INCDIRS  := . ./libleaff ./utility ./libkmer .. ../utility libleaff
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lleaff -lcanu

src/meryl-san/positionDB.mk

@@ -11,7 +11,7 @@ endif
 TARGET   := positionDB
 SOURCES  := positionDB.C
 
-SRC_INCDIRS  := .. ../utility libleaff libkmer
+SRC_INCDIRS  := . ./libleaff ./utility ./libkmer .. ../utility libleaff libkmer
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lleaff -lcanu

src/meryl-san/simple-dump.mk

@@ -11,7 +11,7 @@ endif
 TARGET   := simple-dump
 SOURCES  := simple-dump.C
 
-SRC_INCDIRS  := .. ../utility libleaff libkmer
+SRC_INCDIRS  := . ./libleaff ./utility ./libkmer  .. ../utility libleaff libkmer
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lleaff -lcanu

src/meryl-san/simple.mk

@@ -11,7 +11,7 @@ endif
 TARGET   := simple
 SOURCES  := simple.C
 
-SRC_INCDIRS  := .. ../utility libleaff
+SRC_INCDIRS  := . ./libleaff ./utility ./libkmer .. ../utility libleaff
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lleaff -lcanu