diff --git a/src/bed12ToBed6/Makefile b/src/bed12ToBed6/Makefile index 036bda41da02cc5c5860130af38b2cb715200fb1..e2e1288341db4dac6b027061d9815b3b35bf9b80 100644 --- a/src/bed12ToBed6/Makefile +++ b/src/bed12ToBed6/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$ # ---------------------------------- SOURCES= bed12ToBed6.cpp OBJECTS= $(SOURCES:.cpp=.o) -_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o filetype.o +_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) PROGRAM= bed12ToBed6 diff --git a/src/bedToBam/Makefile b/src/bedToBam/Makefile index 946717a797ffb679cc352121179ed29c8fd5ccdf..2d02b52c44fada715cb75aeb40ad1caac98f03bc 100644 --- a/src/bedToBam/Makefile +++ b/src/bedToBam/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILIT # ---------------------------------- SOURCES= bedToBam.cpp OBJECTS= $(SOURCES:.cpp=.o) -_EXT_OBJECTS=BamWriter.o BGZF.o bedFile.o genomeFile.o lineFileUtilities.o gzstream.o filetype.o +_EXT_OBJECTS=BamWriter.o BGZF.o bedFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) PROGRAM= bedToBam @@ -37,7 +37,7 @@ $(EXT_OBJECTS): @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/ @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/ @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/ - @$(MAKE) -C $(UTILITIES_DIR)/fileType/ + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ clean: @echo "Cleaning up." diff --git a/src/bedToIgv/Makefile b/src/bedToIgv/Makefile index 80970a4135cc799ac2a9b564ebbec6d85dcd40f9..382b8830467bedc5f5225d8d8047ebfe56e69b78 100644 --- a/src/bedToIgv/Makefile +++ b/src/bedToIgv/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILIT # ---------------------------------- SOURCES= bedToIgv.cpp OBJECTS= $(SOURCES:.cpp=.o) -_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o filetype.o +_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) PROGRAM= bedToIgv diff --git a/src/closestBed/Makefile b/src/closestBed/Makefile index ca4f9bdda75accbe77d9ae890789c63a2e251ad8..00cfd889d6af6d88b6eeb88826859f9999cc38b6 100644 --- a/src/closestBed/Makefile +++ b/src/closestBed/Makefile @@ -11,7 +11,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$ # ---------------------------------- SOURCES= closestMain.cpp closestBed.cpp OBJECTS= $(SOURCES:.cpp=.o) -_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o filetype.o +_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) PROGRAM= closestBed diff --git a/src/complementBed/Makefile b/src/complementBed/Makefile index ec79524bad65e2e7c594127a5bf89777bf03cd26..1e980bd6cdb3594347034e1b4e0383ef11815f0b 100644 --- a/src/complementBed/Makefile +++ b/src/complementBed/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILIT # ---------------------------------- SOURCES= complementMain.cpp complementBed.cpp OBJECTS= $(SOURCES:.cpp=.o) -_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o filetype.o +_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) PROGRAM= complementBed diff --git a/src/coverageBed/Makefile b/src/coverageBed/Makefile index 2a93031bf8d93a0488f7d5600147291cef198c2b..722b0c63adbda9687838851b7d1ee9512f2fd8ed 100644 --- a/src/coverageBed/Makefile +++ b/src/coverageBed/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$ # ---------------------------------- SOURCES= coverageMain.cpp coverageBed.cpp OBJECTS= $(SOURCES:.cpp=.o) -_EXT_OBJECTS=bedFile.o lineFileUtilities.o BamReader.o BamAncillary.o BGZF.o gzstream.o filetype.o +_EXT_OBJECTS=bedFile.o lineFileUtilities.o BamReader.o BamAncillary.o BGZF.o gzstream.o fileType.o EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) PROGRAM= coverageBed diff --git a/src/fastaFromBed/Makefile b/src/fastaFromBed/Makefile index 57e0b956e044b911119ed8f52dc025c5578121d5..cd271426f7c6a7753fbecb833aba036c0e319996 100644 --- a/src/fastaFromBed/Makefile +++ b/src/fastaFromBed/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/sequenceUtilities/ -I$ # ---------------------------------- SOURCES= fastaFromBedMain.cpp fastaFromBed.cpp OBJECTS= $(SOURCES:.cpp=.o) -_EXT_OBJECTS=bedFile.o sequenceUtils.o lineFileUtilities.o gzstream.o filetype.o +_EXT_OBJECTS=bedFile.o sequenceUtils.o lineFileUtilities.o gzstream.o fileType.o EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) PROGRAM= fastaFromBed diff --git a/src/genomeCoverageBed/Makefile b/src/genomeCoverageBed/Makefile index 3f39286767ec14b37ac23bfec9e42966a8f27eab..e6f270bc9b93235e9d9c04048ee4e7adb447d767 100644 --- a/src/genomeCoverageBed/Makefile +++ b/src/genomeCoverageBed/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILIT # ---------------------------------- SOURCES= genomeCoverageMain.cpp genomeCoverageBed.cpp OBJECTS= $(SOURCES:.cpp=.o) -_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o BamReader.o BamAncillary.o BGZF.o gzstream.o filetype.o +_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o BamReader.o BamAncillary.o BGZF.o gzstream.o fileType.o EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) PROGRAM= genomeCoverageBed diff --git a/src/groupBy/Makefile b/src/groupBy/Makefile index 6a473836cf154d863cdb521a45cc1cd6a5b2f9bd..515b92f86761e4014dbf905578b8ee119d9ac2bc 100644 --- a/src/groupBy/Makefile +++ b/src/groupBy/Makefile @@ -13,7 +13,7 @@ INCLUDES = -I$(UTILITIES_DIR)/tabFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$ # ---------------------------------- SOURCES= groupBy.cpp OBJECTS= $(SOURCES:.cpp=.o) -_EXT_OBJECTS=tabFile.o lineFileUtilities.o gzstream.o filetype.o +_EXT_OBJECTS=tabFile.o lineFileUtilities.o gzstream.o fileType.o EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) PROGRAM= groupBy diff --git a/src/intersectBed/Makefile b/src/intersectBed/Makefile index 35cc43a318035bc42d4e9578d1f9dd35338b31ae..c4e88a5f064f8b02421834b2676ed2abcb6bc9b7 100644 --- a/src/intersectBed/Makefile +++ b/src/intersectBed/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$ # ---------------------------------- SOURCES= intersectMain.cpp intersectBed.cpp OBJECTS= $(SOURCES:.cpp=.o) -_EXT_OBJECTS=bedFile.o lineFileUtilities.o BamReader.o BamAncillary.o BamWriter.o BGZF.o gzstream.o filetype.o +_EXT_OBJECTS=bedFile.o lineFileUtilities.o BamReader.o BamAncillary.o BamWriter.o BGZF.o gzstream.o fileType.o EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) PROGRAM= intersectBed diff --git a/src/linksBed/Makefile b/src/linksBed/Makefile index 2630fd15a953a75192d21f76e32b9c710684dd83..75317bf20e885fc00e7af6506f90e159474b42d0 100644 --- a/src/linksBed/Makefile +++ b/src/linksBed/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$ # ---------------------------------- SOURCES= linksMain.cpp linksBed.cpp OBJECTS= $(SOURCES:.cpp=.o) -_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o filetype.o +_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) PROGRAM= linksBed diff --git a/src/maskFastaFromBed/Makefile b/src/maskFastaFromBed/Makefile index f3b5ba40b664522d5d494f8b8bed5c320f9b2b91..9b65fc5255774fab8ecf831aae62226066064058 100644 --- a/src/maskFastaFromBed/Makefile +++ b/src/maskFastaFromBed/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/sequenceUtilities/ -I$ # ---------------------------------- SOURCES= maskFastaFromBedMain.cpp maskFastaFromBed.cpp OBJECTS= $(SOURCES:.cpp=.o) -_EXT_OBJECTS=bedFile.o sequenceUtils.o lineFileUtilities.o gzstream.o filetype.o +_EXT_OBJECTS=bedFile.o sequenceUtils.o lineFileUtilities.o gzstream.o fileType.o EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) PROGRAM= maskFastaFromBed diff --git a/src/mergeBed/Makefile b/src/mergeBed/Makefile index 961a1189b2bbce0993d7f1d70ef65742162fb2b0..c6a08b6dae4f95bdfeb7dbefc43de0354698fd1a 100644 --- a/src/mergeBed/Makefile +++ b/src/mergeBed/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$ # ---------------------------------- SOURCES= mergeMain.cpp mergeBed.cpp OBJECTS= $(SOURCES:.cpp=.o) -_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o filetype.o +_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) PROGRAM= mergeBed diff --git a/src/overlap/Makefile b/src/overlap/Makefile index a94cf33fcb7681908509e37913b9786559ad901c..da7da74fa90b28c99f440e8a1a47ebd16d5f5859 100644 --- a/src/overlap/Makefile +++ b/src/overlap/Makefile @@ -13,7 +13,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$ # ---------------------------------- SOURCES= overlap.cpp OBJECTS= $(SOURCES:.cpp=.o) -_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o filetype.o +_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) PROGRAM= overlap diff --git a/src/pairToBed/Makefile b/src/pairToBed/Makefile index 27f21d718f8405d95d8b1f720594c916afd183f9..173975b019afa91accd6fba78d3dad862f55eee0 100644 --- a/src/pairToBed/Makefile +++ b/src/pairToBed/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFilePE/ -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITI # ---------------------------------- SOURCES= pairToBedMain.cpp pairToBed.cpp OBJECTS= $(SOURCES:.cpp=.o) -_EXT_OBJECTS=bedFilePE.o bedFile.o lineFileUtilities.o BamReader.o BamWriter.o BGZF.o gzstream.o filetype.o +_EXT_OBJECTS=bedFilePE.o bedFile.o lineFileUtilities.o BamReader.o BamWriter.o BGZF.o gzstream.o fileType.o EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) PROGRAM= pairToBed diff --git a/src/shuffleBed/Makefile b/src/shuffleBed/Makefile index c5ead63e0edb16957e7cf7088f8aadfd168cb64f..42e6cf975cd5b3e533b58fdb2cf8006ab852586f 100644 --- a/src/shuffleBed/Makefile +++ b/src/shuffleBed/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILIT # ---------------------------------- SOURCES= shuffleBedMain.cpp shuffleBed.cpp OBJECTS= $(SOURCES:.cpp=.o) -_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o filetype.o +_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) PROGRAM= shuffleBed diff --git a/src/slopBed/Makefile b/src/slopBed/Makefile index 2af66e55ef3437fb81fd081d363bd05a49537e31..ba798c52674f88aacb00d2e5e151187d58e87a26 100644 --- a/src/slopBed/Makefile +++ b/src/slopBed/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILIT # ---------------------------------- SOURCES= slopBedMain.cpp slopBed.cpp OBJECTS= $(SOURCES:.cpp=.o) -_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o filetype.o +_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) PROGRAM= slopBed diff --git a/src/sortBed/Makefile b/src/sortBed/Makefile index 5c0eab824d586330dfd0eddd1d8d0b7521456266..c675e68aa40425ab48cd29799a4548b4e1641075 100644 --- a/src/sortBed/Makefile +++ b/src/sortBed/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$ # ---------------------------------- SOURCES= sortMain.cpp sortBed.cpp OBJECTS= $(SOURCES:.cpp=.o) -_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o filetype.o +_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) PROGRAM= sortBed diff --git a/src/subtractBed/Makefile b/src/subtractBed/Makefile index 2fd5d2b7cac6185d968610527700ae3c9f3eaf16..10069702f652cd032bb630572397e38deffb8437 100644 --- a/src/subtractBed/Makefile +++ b/src/subtractBed/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$ # ---------------------------------- SOURCES= subtractMain.cpp subtractBed.cpp OBJECTS= $(SOURCES:.cpp=.o) -_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o filetype.o +_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) PROGRAM= subtractBed diff --git a/src/windowBed/Makefile b/src/windowBed/Makefile index 4f71017e16c79782bb2862a5e24bd2b72084b288..f0634e4442d0efa9ec1133465e2c19e8e9141331 100644 --- a/src/windowBed/Makefile +++ b/src/windowBed/Makefile @@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$ # ---------------------------------- SOURCES= windowMain.cpp windowBed.cpp OBJECTS= $(SOURCES:.cpp=.o) -_EXT_OBJECTS=bedFile.o lineFileUtilities.o BamReader.o BamWriter.o BGZF.o gzstream.o filetype.o +_EXT_OBJECTS=bedFile.o lineFileUtilities.o BamReader.o BamWriter.o BGZF.o gzstream.o fileType.o EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) PROGRAM= windowBed