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Makefile
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......@@ -7,18 +7,22 @@ OSXPKGDIR = ${OSXPKGROOT}/resources/bin
OSXLIBDIR = ${OSXPKGROOT}/resources/lib
SELF = ${shell pwd}/Makefile
MASSIVE_REST_EXP = 22
MASSIVE_ID_EXP = 14
MASSIVE_ID_EXP = 18
MASSIVE_CHROM_EXP = 8
MEASURE128BIT = 'long double'
JPARALLEL = 8
MEGAROW = megarow
TYPICAL = typical
FLOAT128 = float128
ALL_BINARY_TYPES = ${TYPICAL} ${MEGAROW} ${FLOAT128}
DEFAULT_BINARY_TYPE = ${TYPICAL}
export BINARY_TYPE = ${DEFAULT_BINARY_TYPE}
DEBUG_TYPE = ${TYPICAL}
WRAPPERS = $(wildcard ${APPDIR}/conversion/src/wrappers/*)
CWD := $(shell pwd)
BINDIR = bin
BINDIR_MODULE = modules
BINDIR_MODULE_TYPICAL = ${BINDIR_MODULE}/${TYPICAL}
BINDIR_MODULE_MEGAROW = ${BINDIR_MODULE}/${MEGAROW}
default:
ifeq ($(KERNEL), Darwin)
......@@ -39,6 +43,7 @@ all:
$(MAKE) support -f ${SELF}
$(MAKE) typical -f ${SELF}
$(MAKE) megarow -f ${SELF}
$(MAKE) float128 -f ${SELF}
$(MAKE) install_all -f ${SELF}
$(MAKE) symlink_typical -f ${SELF}
......@@ -46,162 +51,149 @@ module_all:
$(MAKE) support -f ${SELF}
$(MAKE) typical -f ${SELF}
$(MAKE) megarow -f ${SELF}
$(MAKE) float128 -f ${SELF}
$(MAKE) install_all -f ${SELF}
$(MAKE) module_binaries -f ${SELF}
float128:
$(MAKE) BINARY_TYPE=$(FLOAT128) MEGAFLAGS="-DMEASURE_TYPE=${MEASURE128BIT}" -f ${SELF}
megarow:
$(MAKE) BINARY_TYPE=$(MEGAROW) BINARY_TYPE_NUM=1 POSTFIX=-$(MEGAROW) MEGAFLAGS="-DREST_EXPONENT=${MASSIVE_REST_EXP} -DID_EXPONENT=${MASSIVE_ID_EXP} -DCHROM_EXPONENT=${MASSIVE_CHROM_EXP}" -f ${SELF}
$(MAKE) BINARY_TYPE=$(MEGAROW) MEGAFLAGS="-DREST_EXPONENT=${MASSIVE_REST_EXP} -DID_EXPONENT=${MASSIVE_ID_EXP} -DCHROM_EXPONENT=${MASSIVE_CHROM_EXP}" -f ${SELF}
typical:
$(MAKE) BINARY_TYPE=$(TYPICAL) BINARY_TYPE_NUM=0 POSTFIX=-$(TYPICAL) -f ${SELF}
$(MAKE) BINARY_TYPE=$(TYPICAL) -f ${SELF}
symlink_typical:
$(eval variablename=`find $(BINDIR)/ -maxdepth 1 -mindepth 1 -type f -name '*$(TYPICAL)' -print0 | xargs -L1 -0 -I{} sh -c 'basename {}'`)
for i in ${variablename}; do \
fooname=`echo $$i | sed 's/-$(TYPICAL)//'`; \
echo $${fooname}; \
ln -sf $$i $(BINDIR)/$${fooname}; \
$(eval SRCNAMES=`find $(BINDIR)/ -maxdepth 1 -mindepth 1 -type f -name '*$(TYPICAL)' -print0 | xargs -L1 -0 -I{} sh -c 'basename {}'`)
for SRCNAME in ${SRCNAMES}; do \
DESTNAME=`echo $$SRCNAME | sed 's/-$(TYPICAL)//'`; \
ln -sf $$SRCNAME $(BINDIR)/$${DESTNAME}; \
done
symlink_megarow:
$(eval variablename=`find $(BINDIR)/ -maxdepth 1 -mindepth 1 -type f -name '*$(MEGAROW)' -print0 | xargs -L1 -0 -I{} sh -c 'basename {}'`)
for i in ${variablename}; do \
fooname=`echo $$i | sed 's/-$(MEGAROW)//'`; \
echo $${fooname}; \
ln -sf $$i $(BINDIR)/$${fooname}; \
$(eval SRCNAMES=`find $(BINDIR)/ -maxdepth 1 -mindepth 1 -type f -name '*$(MEGAROW)' -print0 | xargs -L1 -0 -I{} sh -c 'basename {}'`)
for SRCNAME in ${SRCNAMES}; do \
DESTNAME=`echo $$SRCNAME | sed 's/-$(MEGAROW)//'`; \
ln -sf $$SRCNAME $(BINDIR)/$${DESTNAME}; \
done
symlink_float128:
$(eval SRCNAMES=`find $(BINDIR)/ -maxdepth 1 -mindepth 1 -type f -name '*$(FLOAT128)' -print0 | xargs -L1 -0 -I{} sh -c 'basename {}'`)
for SRCNAME in ${SRCNAMES}; do \
DESTNAME=`echo $$SRCNAME | sed 's/-$(FLOAT128)//'`; \
ln -sf $$SRCNAME $(BINDIR)/$${DESTNAME}; \
done
install: prep_c install_conversion_scripts install_starch_scripts
-cp ${APPDIR}/sort-bed/bin/sort-bed- ${BINDIR}/sort-bed
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-slurm- ${BINDIR}/update-sort-bed-slurm
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-starch-slurm- ${BINDIR}/update-sort-bed-starch-slurm
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-migrate-candidates- ${BINDIR}/update-sort-bed-migrate-candidates
-cp ${APPDIR}/bedops/bin/bedops- ${BINDIR}/bedops
-cp ${APPDIR}/closestfeats/bin/closest-features- ${BINDIR}/closest-features
-cp ${APPDIR}/bedmap/bin/bedmap- ${BINDIR}/bedmap
-cp ${APPDIR}/bedextract/bin/bedextract- ${BINDIR}/bedextract
-cp ${APPDIR}/starch/bin/starch- ${BINDIR}/starch
-cp ${APPDIR}/starch/bin/unstarch- ${BINDIR}/unstarch
-cp ${APPDIR}/starch/bin/starchcat- ${BINDIR}/starchcat
-cp ${APPDIR}/starch/bin/starchstrip- ${BINDIR}/starchstrip
-cp ${APPDIR}/conversion/bin/convert2bed- ${BINDIR}/convert2bed
install_all: install_conversion_scripts_with_suffix install_starch_scripts_with_suffix
-cp ${APPDIR}/sort-bed/bin/sort-bed-$(MEGAROW) ${BINDIR}/sort-bed-$(MEGAROW)
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-slurm-$(MEGAROW) ${BINDIR}/update-sort-bed-slurm-$(MEGAROW)
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-starch-slurm-$(MEGAROW) ${BINDIR}/update-sort-bed-starch-slurm-$(MEGAROW)
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-migrate-candidates-$(MEGAROW) ${BINDIR}/update-sort-bed-migrate-candidates-$(MEGAROW)
-cp ${APPDIR}/bedops/bin/bedops-$(MEGAROW) ${BINDIR}/bedops-$(MEGAROW)
-cp ${APPDIR}/closestfeats/bin/closest-features-$(MEGAROW) ${BINDIR}/closest-features-$(MEGAROW)
-cp ${APPDIR}/bedmap/bin/bedmap-$(MEGAROW) ${BINDIR}/bedmap-$(MEGAROW)
-cp ${APPDIR}/bedextract/bin/bedextract-$(MEGAROW) ${BINDIR}/bedextract-$(MEGAROW)
-cp ${APPDIR}/starch/bin/starch-$(MEGAROW) ${BINDIR}/starch-$(MEGAROW)
-cp ${APPDIR}/starch/bin/unstarch-$(MEGAROW) ${BINDIR}/unstarch-$(MEGAROW)
-cp ${APPDIR}/starch/bin/starchcat-$(MEGAROW) ${BINDIR}/starchcat-$(MEGAROW)
-cp ${APPDIR}/starch/bin/starchstrip-$(MEGAROW) ${BINDIR}/starchstrip-$(MEGAROW)
-cp ${APPDIR}/conversion/bin/convert2bed-$(MEGAROW) ${BINDIR}/convert2bed-$(MEGAROW)
-cp ${APPDIR}/sort-bed/bin/sort-bed-$(TYPICAL) ${BINDIR}/sort-bed-$(TYPICAL)
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-slurm-$(TYPICAL) ${BINDIR}/update-sort-bed-slurm-$(TYPICAL)
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-starch-slurm-$(TYPICAL) ${BINDIR}/update-sort-bed-starch-slurm-$(TYPICAL)
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-migrate-candidates-$(TYPICAL) ${BINDIR}/update-sort-bed-migrate-candidates-$(TYPICAL)
-cp ${APPDIR}/bedops/bin/bedops-$(TYPICAL) ${BINDIR}/bedops-$(TYPICAL)
-cp ${APPDIR}/closestfeats/bin/closest-features-$(TYPICAL) ${BINDIR}/closest-features-$(TYPICAL)
-cp ${APPDIR}/bedmap/bin/bedmap-$(TYPICAL) ${BINDIR}/bedmap-$(TYPICAL)
-cp ${APPDIR}/bedextract/bin/bedextract-$(TYPICAL) ${BINDIR}/bedextract-$(TYPICAL)
-cp ${APPDIR}/starch/bin/starch-$(TYPICAL) ${BINDIR}/starch-$(TYPICAL)
-cp ${APPDIR}/starch/bin/unstarch-$(TYPICAL) ${BINDIR}/unstarch-$(TYPICAL)
-cp ${APPDIR}/starch/bin/starchcat-$(TYPICAL) ${BINDIR}/starchcat-$(TYPICAL)
-cp ${APPDIR}/starch/bin/starchstrip-$(TYPICAL) ${BINDIR}/starchstrip-$(TYPICAL)
-cp ${APPDIR}/conversion/bin/convert2bed-$(TYPICAL) ${BINDIR}/convert2bed-$(TYPICAL)
-cp ${OTHERDIR}/switch-BEDOPS-binary-type ${BINDIR}/switch-BEDOPS-binary-type
-cp ${APPDIR}/sort-bed/bin/sort-bed-${TYPICAL} ${BINDIR}/sort-bed
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-slurm-${TYPICAL} ${BINDIR}/update-sort-bed-slurm
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-starch-slurm-${TYPICAL} ${BINDIR}/update-sort-bed-starch-slurm
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-migrate-candidates-${TYPICAL} ${BINDIR}/update-sort-bed-migrate-candidates
-cp ${APPDIR}/bedops/bin/bedops-${TYPICAL} ${BINDIR}/bedops
-cp ${APPDIR}/closestfeats/bin/closest-features-${TYPICAL} ${BINDIR}/closest-features
-cp ${APPDIR}/bedmap/bin/bedmap-${TYPICAL} ${BINDIR}/bedmap
-cp ${APPDIR}/bedextract/bin/bedextract-${TYPICAL} ${BINDIR}/bedextract
-cp ${APPDIR}/starch/bin/starch-${TYPICAL} ${BINDIR}/starch
-cp ${APPDIR}/starch/bin/unstarch-${TYPICAL} ${BINDIR}/unstarch
-cp ${APPDIR}/starch/bin/starchcat-${TYPICAL} ${BINDIR}/starchcat
-cp ${APPDIR}/starch/bin/starchstrip-${TYPICAL} ${BINDIR}/starchstrip
-cp ${APPDIR}/conversion/bin/convert2bed-${TYPICAL} ${BINDIR}/convert2bed
install_float128: prep_c install_conversion_scripts
-cp ${APPDIR}/sort-bed/bin/sort-bed-${FLOAT128} ${BINDIR}/sort-bed
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-slurm-${FLOAT128} ${BINDIR}/update-sort-bed-slurm
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-starch-slurm-${FLOAT128} ${BINDIR}/update-sort-bed-starch-slurm
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-migrate-candidates-${FLOAT128} ${BINDIR}/update-sort-bed-migrate-candidates
-cp ${APPDIR}/bedops/bin/bedops-${FLOAT128} ${BINDIR}/bedops
-cp ${APPDIR}/closestfeats/bin/closest-features-${FLOAT128} ${BINDIR}/closest-features
-cp ${APPDIR}/bedmap/bin/bedmap-${FLOAT128} ${BINDIR}/bedmap
-cp ${APPDIR}/bedextract/bin/bedextract-${FLOAT128} ${BINDIR}/bedextract
-cp ${APPDIR}/starch/bin/starch-${FLOAT128} ${BINDIR}/starch
-cp ${APPDIR}/starch/bin/unstarch-${FLOAT128} ${BINDIR}/unstarch
-cp ${APPDIR}/starch/bin/starchcat-${FLOAT128} ${BINDIR}/starchcat
-cp ${APPDIR}/starch/bin/starchstrip-${FLOAT128} ${BINDIR}/starchstrip
-cp ${APPDIR}/conversion/bin/convert2bed-${FLOAT128} ${BINDIR}/convert2bed
install_megarow: prep_c install_conversion_scripts
-cp ${APPDIR}/sort-bed/bin/sort-bed-${MEGAROW} ${BINDIR}/sort-bed
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-slurm-${MEGAROW} ${BINDIR}/update-sort-bed-slurm
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-starch-slurm-${MEGAROW} ${BINDIR}/update-sort-bed-starch-slurm
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-migrate-candidates-${MEGAROW} ${BINDIR}/update-sort-bed-migrate-candidates
-cp ${APPDIR}/bedops/bin/bedops-${MEGAROW} ${BINDIR}/bedops
-cp ${APPDIR}/closestfeats/bin/closest-features-${MEGAROW} ${BINDIR}/closest-features
-cp ${APPDIR}/bedmap/bin/bedmap-${MEGAROW} ${BINDIR}/bedmap
-cp ${APPDIR}/bedextract/bin/bedextract-${MEGAROW} ${BINDIR}/bedextract
-cp ${APPDIR}/starch/bin/starch-${MEGAROW} ${BINDIR}/starch
-cp ${APPDIR}/starch/bin/unstarch-${MEGAROW} ${BINDIR}/unstarch
-cp ${APPDIR}/starch/bin/starchcat-${MEGAROW} ${BINDIR}/starchcat
-cp ${APPDIR}/starch/bin/starchstrip-${MEGAROW} ${BINDIR}/starchstrip
-cp ${APPDIR}/conversion/bin/convert2bed-${MEGAROW} ${BINDIR}/convert2bed
install_all: prep_c install_conversion_scripts_all install_starch_scripts_all
for btype in ${ALL_BINARY_TYPES}; do \
cp ${APPDIR}/sort-bed/bin/sort-bed-$$btype ${BINDIR}/sort-bed-$$btype; \
cp ${APPDIR}/sort-bed/bin/update-sort-bed-slurm-$$btype ${BINDIR}/update-sort-bed-slurm-$$btype; \
cp ${APPDIR}/sort-bed/bin/update-sort-bed-starch-slurm-$$btype ${BINDIR}/update-sort-bed-starch-slurm-$$btype; \
cp ${APPDIR}/sort-bed/bin/update-sort-bed-migrate-candidates-$$btype ${BINDIR}/update-sort-bed-migrate-candidates-$$btype; \
cp ${APPDIR}/bedops/bin/bedops-$$btype ${BINDIR}/bedops-$$btype; \
cp ${APPDIR}/closestfeats/bin/closest-features-$$btype ${BINDIR}/closest-features-$$btype; \
cp ${APPDIR}/bedmap/bin/bedmap-$$btype ${BINDIR}/bedmap-$$btype; \
cp ${APPDIR}/bedextract/bin/bedextract-$$btype ${BINDIR}/bedextract-$$btype; \
cp ${APPDIR}/starch/bin/starch-$$btype ${BINDIR}/starch-$$btype; \
cp ${APPDIR}/starch/bin/unstarch-$$btype ${BINDIR}/unstarch-$$btype; \
cp ${APPDIR}/starch/bin/starchcat-$$btype ${BINDIR}/starchcat-$$btype; \
cp ${APPDIR}/starch/bin/starchstrip-$$btype ${BINDIR}/starchstrip-$$btype; \
cp ${APPDIR}/conversion/bin/convert2bed-$$btype ${BINDIR}/convert2bed-$$btype; \
done
-cp ${OTHERDIR}/switch-BEDOPS-binary-type ${BINDIR}
module_binaries:
mkdir -p ${BINDIR_MODULE_TYPICAL}
-cp ${BINDIR}/sort-bed-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/sort-bed
-cp ${BINDIR}/update-sort-bed-slurm-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/update-sort-bed-slurm
-cp ${BINDIR}/update-sort-bed-starch-slurm-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/update-sort-bed-starch-slurm
-cp ${BINDIR}/update-sort-bed-migrate-candidates-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/update-sort-bed-migrate-candidates
-cp ${BINDIR}/bedops-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/bedops
-cp ${BINDIR}/closest-features-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/closest-features
-cp ${BINDIR}/bedmap-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/bedmap
-cp ${BINDIR}/bedextract-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/bedextract
-cp ${BINDIR}/starch-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/starch
-cp ${BINDIR}/unstarch-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/unstarch
-cp ${BINDIR}/starchcat-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/starchcat
-cp ${BINDIR}/starchstrip-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/starchstrip
-cp ${BINDIR}/starch-diff-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/starch-diff
-cp ${BINDIR}/convert2bed-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/convert2bed
-cp ${BINDIR}/bam2bed-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/bam2bed
-cp ${BINDIR}/gff2bed-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/gff2bed
-cp ${BINDIR}/gtf2bed-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/gtf2bed
-cp ${BINDIR}/gvf2bed-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/gvf2bed
-cp ${BINDIR}/psl2bed-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/psl2bed
-cp ${BINDIR}/rmsk2bed-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/rmsk2bed
-cp ${BINDIR}/sam2bed-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/sam2bed
-cp ${BINDIR}/vcf2bed-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/vcf2bed
-cp ${BINDIR}/wig2bed-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/wig2bed
-cp ${BINDIR}/bam2starch-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/bam2starch
-cp ${BINDIR}/gff2starch-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/gff2starch
-cp ${BINDIR}/gtf2starch-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/gtf2starch
-cp ${BINDIR}/gvf2starch-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/gvf2starch
-cp ${BINDIR}/psl2starch-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/psl2starch
-cp ${BINDIR}/rmsk2starch-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/rmsk2starch
-cp ${BINDIR}/sam2starch-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/sam2starch
-cp ${BINDIR}/vcf2starch-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/vcf2starch
-cp ${BINDIR}/wig2starch-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/wig2starch
-cp ${BINDIR}/bam2bed_sge-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/bam2bed_sge
-cp ${BINDIR}/bam2bed_slurm-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/bam2bed_slurm
-cp ${BINDIR}/bam2bed_gnuParallel-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/bam2bed_gnuParallel
-cp ${BINDIR}/bam2starch_sge-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/bam2starch_sge
-cp ${BINDIR}/bam2starch_slurm-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/bam2starch_slurm
-cp ${BINDIR}/bam2starch_gnuParallel-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/bam2starch_gnuParallel
-cp ${BINDIR}/starchcluster_sge-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/starchcluster_sge
-cp ${BINDIR}/starchcluster_gnuParallel-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/starchcluster_gnuParallel
-cp ${BINDIR}/starchcluster_slurm-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/starchcluster_slurm
-cp ${BINDIR}/starch-diff-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/starch-diff
mkdir -p ${BINDIR_MODULE_MEGAROW}
-cp ${BINDIR}/sort-bed-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/sort-bed
-cp ${BINDIR}/update-sort-bed-slurm-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/update-sort-bed-slurm
-cp ${BINDIR}/update-sort-bed-starch-slurm-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/update-sort-bed-starch-slurm
-cp ${BINDIR}/update-sort-bed-migrate-candidates-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/update-sort-bed-migrate-candidates
-cp ${BINDIR}/bedops-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/bedops
-cp ${BINDIR}/closest-features-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/closest-features
-cp ${BINDIR}/bedmap-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/bedmap
-cp ${BINDIR}/bedextract-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/bedextract
-cp ${BINDIR}/starch-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/starch
-cp ${BINDIR}/unstarch-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/unstarch
-cp ${BINDIR}/starchcat-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/starchcat
-cp ${BINDIR}/starchstrip-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/starchstrip
-cp ${BINDIR}/starch-diff-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/starch-diff
-cp ${BINDIR}/convert2bed-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/convert2bed
-cp ${BINDIR}/bam2bed-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/bam2bed
-cp ${BINDIR}/gff2bed-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/gff2bed
-cp ${BINDIR}/gtf2bed-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/gtf2bed
-cp ${BINDIR}/gvf2bed-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/gvf2bed
-cp ${BINDIR}/psl2bed-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/psl2bed
-cp ${BINDIR}/rmsk2bed-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/rmsk2bed
-cp ${BINDIR}/sam2bed-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/sam2bed
-cp ${BINDIR}/vcf2bed-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/vcf2bed
-cp ${BINDIR}/wig2bed-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/wig2bed
-cp ${BINDIR}/bam2starch-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/bam2starch
-cp ${BINDIR}/gff2starch-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/gff2starch
-cp ${BINDIR}/gtf2starch-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/gtf2starch
-cp ${BINDIR}/gvf2starch-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/gvf2starch
-cp ${BINDIR}/psl2starch-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/psl2starch
-cp ${BINDIR}/rmsk2starch-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/rmsk2starch
-cp ${BINDIR}/sam2starch-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/sam2starch
-cp ${BINDIR}/vcf2starch-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/vcf2starch
-cp ${BINDIR}/wig2starch-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/wig2starch
-cp ${BINDIR}/bam2bed_sge-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/bam2bed_sge
-cp ${BINDIR}/bam2bed_slurm-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/bam2bed_slurm
-cp ${BINDIR}/bam2bed_gnuParallel-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/bam2bed_gnuParallel
-cp ${BINDIR}/bam2starch_sge-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/bam2starch_sge
-cp ${BINDIR}/bam2starch_slurm-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/bam2starch_slurm
-cp ${BINDIR}/bam2starch_gnuParallel-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/bam2starch_gnuParallel
-cp ${BINDIR}/starchcluster_sge-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/starchcluster_sge
-cp ${BINDIR}/starchcluster_gnuParallel-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/starchcluster_gnuParallel
-cp ${BINDIR}/starchcluster_slurm-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/starchcluster_slurm
-cp ${BINDIR}/starch-diff-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/starch-diff
for btype in ${ALL_BINARY_TYPES}; do \
mkdir -p ${BINDIR_MODULE}/$$btype; \
cp ${BINDIR}/sort-bed-$$btype ${BINDIR_MODULE}/$$btype/sort-bed; \
cp ${BINDIR}/update-sort-bed-slurm-$$btype ${BINDIR_MODULE}/$$btype/update-sort-bed-slurm; \
cp ${BINDIR}/update-sort-bed-starch-slurm-$$btype ${BINDIR_MODULE}/$$btype/update-sort-bed-starch-slurm; \
cp ${BINDIR}/update-sort-bed-migrate-candidates-$$btype ${BINDIR_MODULE}/$$btype/update-sort-bed-migrate-candidates; \
cp ${BINDIR}/bedops-$$btype ${BINDIR_MODULE}/$$btype/bedops; \
cp ${BINDIR}/closest-features-$$btype ${BINDIR_MODULE}/$$btype/closest-features; \
cp ${BINDIR}/bedmap-$$btype ${BINDIR_MODULE}/$$btype/bedmap; \
cp ${BINDIR}/bedextract-$$btype ${BINDIR_MODULE}/$$btype/bedextract; \
cp ${BINDIR}/starch-$$btype ${BINDIR_MODULE}/$$btype/starch; \
cp ${BINDIR}/unstarch-$$btype ${BINDIR_MODULE}/$$btype/unstarch; \
cp ${BINDIR}/starchcat-$$btype ${BINDIR_MODULE}/$$btype/starchcat; \
cp ${BINDIR}/starchstrip-$$btype ${BINDIR_MODULE}/$$btype/starchstrip; \
cp ${BINDIR}/starch-diff-$$btype ${BINDIR_MODULE}/$$btype/starch-diff; \
cp ${BINDIR}/convert2bed-$$btype ${BINDIR_MODULE}/$$btype/convert2bed; \
cp ${BINDIR}/bam2bed-$$btype ${BINDIR_MODULE}/$$btype/bam2bed; \
cp ${BINDIR}/gff2bed-$$btype ${BINDIR_MODULE}/$$btype/gff2bed; \
cp ${BINDIR}/gtf2bed-$$btype ${BINDIR_MODULE}/$$btype/gtf2bed; \
cp ${BINDIR}/gvf2bed-$$btype ${BINDIR_MODULE}/$$btype/gvf2bed; \
cp ${BINDIR}/psl2bed-$$btype ${BINDIR_MODULE}/$$btype/psl2bed; \
cp ${BINDIR}/rmsk2bed-$$btype ${BINDIR_MODULE}/$$btype/rmsk2bed; \
cp ${BINDIR}/sam2bed-$$btype ${BINDIR_MODULE}/$$btype/sam2bed; \
cp ${BINDIR}/vcf2bed-$$btype ${BINDIR_MODULE}/$$btype/vcf2bed; \
cp ${BINDIR}/wig2bed-$$btype ${BINDIR_MODULE}/$$btype/wig2bed; \
cp ${BINDIR}/bam2starch-$$btype ${BINDIR_MODULE}/$$btype/bam2starch; \
cp ${BINDIR}/gff2starch-$$btype ${BINDIR_MODULE}/$$btype/gff2starch; \
cp ${BINDIR}/gtf2starch-$$btype ${BINDIR_MODULE}/$$btype/gtf2starch; \
cp ${BINDIR}/gvf2starch-$$btype ${BINDIR_MODULE}/$$btype/gvf2starch; \
cp ${BINDIR}/psl2starch-$$btype ${BINDIR_MODULE}/$$btype/psl2starch; \
cp ${BINDIR}/rmsk2starch-$$btype ${BINDIR_MODULE}/$$btype/rmsk2starch; \
cp ${BINDIR}/sam2starch-$$btype ${BINDIR_MODULE}/$$btype/sam2starch; \
cp ${BINDIR}/vcf2starch-$$btype ${BINDIR_MODULE}/$$btype/vcf2starch; \
cp ${BINDIR}/wig2starch-$$btype ${BINDIR_MODULE}/$$btype/wig2starch; \
cp ${BINDIR}/bam2bed_sge-$$btype ${BINDIR_MODULE}/$$btype/bam2bed_sge; \
cp ${BINDIR}/bam2bed_slurm-$$btype ${BINDIR_MODULE}/$$btype/bam2bed_slurm; \
cp ${BINDIR}/bam2bed_gnuParallel-$$btype ${BINDIR_MODULE}/$$btype/bam2bed_gnuParallel; \
cp ${BINDIR}/bam2starch_sge-$$btype ${BINDIR_MODULE}/$$btype/bam2starch_sge; \
cp ${BINDIR}/bam2starch_slurm-$$btype ${BINDIR_MODULE}/$$btype/bam2starch_slurm; \
cp ${BINDIR}/bam2starch_gnuParallel-$$btype ${BINDIR_MODULE}/$$btype/bam2starch_gnuParallel; \
cp ${BINDIR}/starchcluster_sge-$$btype ${BINDIR_MODULE}/$$btype/starchcluster_sge; \
cp ${BINDIR}/starchcluster_gnuParallel-$$btype ${BINDIR_MODULE}/$$btype/starchcluster_gnuParallel; \
cp ${BINDIR}/starchcluster_slurm-$$btype ${BINDIR_MODULE}/$$btype/starchcluster_slurm; \
cp ${BINDIR}/starch-diff-$$btype ${BINDIR_MODULE}/$$btype/starch-diff; \
done
#######################
# install details
......@@ -210,42 +202,30 @@ prep_c:
mkdir -p ${BINDIR}
install_debug: prep_c install_conversion_scripts install_starch_scripts
-cp ${APPDIR}/sort-bed/bin/debug.sort-bed- ${BINDIR}/debug.sort-bed
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-slurm- ${BINDIR}/update-sort-bed-slurm
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-starch-slurm- ${BINDIR}/update-sort-bed-starch-slurm
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-migrate-candidates- ${BINDIR}/update-sort-bed-migrate-candidates
-cp ${APPDIR}/bedops/bin/debug.bedops- ${BINDIR}/debug.bedops
-cp ${APPDIR}/closestfeats/bin/debug.closest-features- ${BINDIR}/debug.closest-features
-cp ${APPDIR}/bedmap/bin/debug.bedmap- ${BINDIR}/debug.bedmap
-cp ${APPDIR}/bedextract/bin/debug.bedextract- ${BINDIR}/debug.bedextract
-cp ${APPDIR}/starch/bin/debug.starch- ${BINDIR}/debug.starch
-cp ${APPDIR}/starch/bin/debug.unstarch- ${BINDIR}/debug.unstarch
-cp ${APPDIR}/starch/bin/debug.starchcat- ${BINDIR}/debug.starchcat
-cp ${APPDIR}/starch/bin/debug.starchstrip- ${BINDIR}/debug.starchstrip
-cp ${APPDIR}/conversion/bin/debug.convert2bed- ${BINDIR}/debug.convert2bed
find ${APPDIR}/ -maxdepth 4 -mindepth 1 -type f -name 'debug.*${DEBUG_TYPE}' -exec cp {} ${BINDIR} \;
install_gprof: prep_c install_conversion_scripts install_starch_scripts
-cp ${APPDIR}/sort-bed/bin/gprof.sort-bed- ${BINDIR}/gprof.sort-bed
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-slurm- ${BINDIR}/update-sort-bed-slurm
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-starch-slurm- ${BINDIR}/update-sort-bed-starch-slurm
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-migrate-candidates- ${BINDIR}/update-sort-bed-migrate-candidates
-cp ${APPDIR}/bedops/bin/gprof.bedops- ${BINDIR}/gprof.bedops
-cp ${APPDIR}/closestfeats/bin/gprof.closest-features- ${BINDIR}/gprof.closest-features
-cp ${APPDIR}/bedmap/bin/gprof.bedmap- ${BINDIR}/gprof.bedmap
-cp ${APPDIR}/bedextract/bin/gprof.bedextract- ${BINDIR}/gprof.bedextract
-cp ${APPDIR}/starch/bin/gprof.starch- ${BINDIR}/gprof.starch
-cp ${APPDIR}/starch/bin/gprof.unstarch- ${BINDIR}/gprof.unstarch
-cp ${APPDIR}/starch/bin/gprof.starchcat- ${BINDIR}/gprof.starchcat
-cp ${APPDIR}/starch/bin/gprof.starchstrip- ${BINDIR}/gprof.starchstrip
-cp ${APPDIR}/conversion/bin/gprof.convert2bed- ${BINDIR}/gprof.convert2bed
-cp ${APPDIR}/sort-bed/bin/gprof.sort-bed ${BINDIR}/gprof.sort-bed
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-slurm ${BINDIR}/update-sort-bed-slurm
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-starch-slurm ${BINDIR}/update-sort-bed-starch-slurm
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-migrate-candidates ${BINDIR}/update-sort-bed-migrate-candidates
-cp ${APPDIR}/bedops/bin/gprof.bedops ${BINDIR}/gprof.bedops
-cp ${APPDIR}/closestfeats/bin/gprof.closest-features ${BINDIR}/gprof.closest-features
-cp ${APPDIR}/bedmap/bin/gprof.bedmap ${BINDIR}/gprof.bedmap
-cp ${APPDIR}/bedextract/bin/gprof.bedextract ${BINDIR}/gprof.bedextract
-cp ${APPDIR}/starch/bin/gprof.starch ${BINDIR}/gprof.starch
-cp ${APPDIR}/starch/bin/gprof.unstarch ${BINDIR}/gprof.unstarch
-cp ${APPDIR}/starch/bin/gprof.starchcat ${BINDIR}/gprof.starchcat
-cp ${APPDIR}/starch/bin/gprof.starchstrip ${BINDIR}/gprof.starchstrip
-cp ${APPDIR}/conversion/bin/gprof.convert2bed ${BINDIR}/gprof.convert2bed
install_starch_scripts: prep_c
-cp ${APPDIR}/starch/bin/starchcluster_sge- ${BINDIR}/starchcluster_sge
-cp ${APPDIR}/starch/bin/starchcluster_gnuParallel- ${BINDIR}/starchcluster_gnuParallel
-cp ${APPDIR}/starch/bin/starchcluster_slurm- ${BINDIR}/starchcluster_slurm
-cp ${APPDIR}/starch/bin/starch-diff- ${BINDIR}/starch-diff
-cp ${APPDIR}/starch/bin/starchcluster_sge-$(TYPICAL) ${BINDIR}/starchcluster_sge
-cp ${APPDIR}/starch/bin/starchcluster_gnuParallel-$(TYPICAL) ${BINDIR}/starchcluster_gnuParallel
-cp ${APPDIR}/starch/bin/starchcluster_slurm-$(TYPICAL) ${BINDIR}/starchcluster_slurm
-cp ${APPDIR}/starch/bin/starch-diff-$(TYPICAL) ${BINDIR}/starch-diff
install_starch_scripts_with_suffix: prep_c
install_starch_scripts_all: prep_c
-cp ${APPDIR}/starch/bin/starchcluster_sge-$(TYPICAL) ${BINDIR}/starchcluster_sge-$(TYPICAL)
-cp ${APPDIR}/starch/bin/starchcluster_gnuParallel-$(TYPICAL) ${BINDIR}/starchcluster_gnuParallel-$(TYPICAL)
-cp ${APPDIR}/starch/bin/starchcluster_slurm-$(TYPICAL) ${BINDIR}/starchcluster_slurm-$(TYPICAL)
......@@ -254,77 +234,76 @@ install_starch_scripts_with_suffix: prep_c
-cp ${APPDIR}/starch/bin/starchcluster_gnuParallel-$(MEGAROW) ${BINDIR}/starchcluster_gnuParallel-$(MEGAROW)
-cp ${APPDIR}/starch/bin/starchcluster_slurm-$(MEGAROW) ${BINDIR}/starchcluster_slurm-$(MEGAROW)
-cp ${APPDIR}/starch/bin/starch-diff-$(MEGAROW) ${BINDIR}/starch-diff-$(MEGAROW)
-cp ${APPDIR}/starch/bin/starchcluster_sge-$(MEGAROW) ${BINDIR}/starchcluster_sge-$(FLOAT128)
-cp ${APPDIR}/starch/bin/starchcluster_gnuParallel-$(MEGAROW) ${BINDIR}/starchcluster_gnuParallel-$(FLOAT128)
-cp ${APPDIR}/starch/bin/starchcluster_slurm-$(MEGAROW) ${BINDIR}/starchcluster_slurm-$(FLOAT128)
-cp ${APPDIR}/starch/bin/starch-diff-$(MEGAROW) ${BINDIR}/starch-diff-$(FLOAT128)
install_conversion_scripts: prep_c
-cp ${APPDIR}/conversion/src/wrappers/bam2bed ${BINDIR}/bam2bed
-cp ${APPDIR}/conversion/src/wrappers/gff2bed ${BINDIR}/gff2bed
-cp ${APPDIR}/conversion/src/wrappers/gtf2bed ${BINDIR}/gtf2bed
-cp ${APPDIR}/conversion/src/wrappers/gvf2bed ${BINDIR}/gvf2bed
-cp ${APPDIR}/conversion/src/wrappers/psl2bed ${BINDIR}/psl2bed
-cp ${APPDIR}/conversion/src/wrappers/rmsk2bed ${BINDIR}/rmsk2bed
-cp ${APPDIR}/conversion/src/wrappers/sam2bed ${BINDIR}/sam2bed
-cp ${APPDIR}/conversion/src/wrappers/vcf2bed ${BINDIR}/vcf2bed
-cp ${APPDIR}/conversion/src/wrappers/wig2bed ${BINDIR}/wig2bed
-cp ${APPDIR}/conversion/src/wrappers/bam2starch ${BINDIR}/bam2starch
-cp ${APPDIR}/conversion/src/wrappers/gff2starch ${BINDIR}/gff2starch
-cp ${APPDIR}/conversion/src/wrappers/gtf2starch ${BINDIR}/gtf2starch
-cp ${APPDIR}/conversion/src/wrappers/gvf2starch ${BINDIR}/gvf2starch
-cp ${APPDIR}/conversion/src/wrappers/psl2starch ${BINDIR}/psl2starch
-cp ${APPDIR}/conversion/src/wrappers/rmsk2starch ${BINDIR}/rmsk2starch
-cp ${APPDIR}/conversion/src/wrappers/sam2starch ${BINDIR}/sam2starch
-cp ${APPDIR}/conversion/src/wrappers/vcf2starch ${BINDIR}/vcf2starch
-cp ${APPDIR}/conversion/src/wrappers/wig2starch ${BINDIR}/wig2starch
-cp ${APPDIR}/conversion/src/wrappers/bam2bed_sge ${BINDIR}/bam2bed_sge
-cp ${APPDIR}/conversion/src/wrappers/bam2bed_slurm ${BINDIR}/bam2bed_slurm
-cp ${APPDIR}/conversion/src/wrappers/bam2bed_gnuParallel ${BINDIR}/bam2bed_gnuParallel
-cp ${APPDIR}/conversion/src/wrappers/bam2starch_sge ${BINDIR}/bam2starch_sge
-cp ${APPDIR}/conversion/src/wrappers/bam2starch_slurm ${BINDIR}/bam2starch_slurm
-cp ${APPDIR}/conversion/src/wrappers/bam2starch_gnuParallel ${BINDIR}/bam2starch_gnuParallel
cp $(WRAPPERS) ${BINDIR}
.PHONY: $(WRAPPERS)
install_conversion_scripts_with_suffix: $(WRAPPERS)
install_conversion_scripts_all: $(WRAPPERS)
$(WRAPPERS): prep_c
cp $@ $(patsubst %,$(BINDIR)/%-$(TYPICAL), $(notdir $@))
cp $@ $(patsubst %,$(BINDIR)/%-$(MEGAROW), $(notdir $@))
cp $@ $(patsubst %,$(BINDIR)/%-$(FLOAT128), $(notdir $@))
install_osx_packaging_bins: prep_c all
mkdir -p ${OSXPKGDIR}
-cp ${APPDIR}/sort-bed/bin/sort-bed-typical ${OSXPKGDIR}/sort-bed-typical
-cp ${APPDIR}/sort-bed/bin/sort-bed-megarow ${OSXPKGDIR}/sort-bed-megarow
-cp ${APPDIR}/sort-bed/bin/sort-bed-float128 ${OSXPKGDIR}/sort-bed-float128
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-slurm-typical ${OSXPKGDIR}/update-sort-bed-slurm-typical
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-slurm-megarow ${OSXPKGDIR}/update-sort-bed-slurm-megarow
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-slurm-float128 ${OSXPKGDIR}/update-sort-bed-slurm-float128
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-starch-slurm-typical ${OSXPKGDIR}/update-sort-bed-starch-slurm-typical
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-starch-slurm-megarow ${OSXPKGDIR}/update-sort-bed-starch-slurm-megarow
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-starch-slurm-float128 ${OSXPKGDIR}/update-sort-bed-starch-slurm-float128
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-migrate-candidates-typical ${OSXPKGDIR}/update-sort-bed-migrate-candidates-typical
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-migrate-candidates-megarow ${OSXPKGDIR}/update-sort-bed-migrate-candidates-megarow
-cp ${APPDIR}/sort-bed/bin/update-sort-bed-migrate-candidates-float128 ${OSXPKGDIR}/update-sort-bed-migrate-candidates-float128
-cp ${APPDIR}/bedops/bin/bedops-typical ${OSXPKGDIR}/bedops-typical
-cp ${APPDIR}/bedops/bin/bedops-megarow ${OSXPKGDIR}/bedops-megarow
-cp ${APPDIR}/bedops/bin/bedops-float128 ${OSXPKGDIR}/bedops-float128
-cp ${APPDIR}/closestfeats/bin/closest-features-typical ${OSXPKGDIR}/closest-features-typical
-cp ${APPDIR}/closestfeats/bin/closest-features-megarow ${OSXPKGDIR}/closest-features-megarow
-cp ${APPDIR}/closestfeats/bin/closest-features-float128 ${OSXPKGDIR}/closest-features-float128
-cp ${APPDIR}/bedmap/bin/bedmap-typical ${OSXPKGDIR}/bedmap-typical
-cp ${APPDIR}/bedmap/bin/bedmap-megarow ${OSXPKGDIR}/bedmap-megarow
-cp ${APPDIR}/bedmap/bin/bedmap-float128 ${OSXPKGDIR}/bedmap-float128
-cp ${APPDIR}/bedextract/bin/bedextract-typical ${OSXPKGDIR}/bedextract-typical
-cp ${APPDIR}/bedextract/bin/bedextract-megarow ${OSXPKGDIR}/bedextract-megarow
-cp ${APPDIR}/bedextract/bin/bedextract-float128 ${OSXPKGDIR}/bedextract-float128
-cp ${APPDIR}/starch/bin/starch-typical ${OSXPKGDIR}/starch-typical
-cp ${APPDIR}/starch/bin/starch-megarow ${OSXPKGDIR}/starch-megarow
-cp ${APPDIR}/starch/bin/starch-float128 ${OSXPKGDIR}/starch-float128
-cp ${APPDIR}/starch/bin/unstarch-typical ${OSXPKGDIR}/unstarch-typical
-cp ${APPDIR}/starch/bin/unstarch-megarow ${OSXPKGDIR}/unstarch-megarow
-cp ${APPDIR}/starch/bin/unstarch-float128 ${OSXPKGDIR}/unstarch-float128
-cp ${APPDIR}/starch/bin/starchcat-typical ${OSXPKGDIR}/starchcat-typical
-cp ${APPDIR}/starch/bin/starchcat-megarow ${OSXPKGDIR}/starchcat-megarow
-cp ${APPDIR}/starch/bin/starchcat-float128 ${OSXPKGDIR}/starchcat-float128
-cp ${APPDIR}/starch/bin/starchstrip-typical ${OSXPKGDIR}/starchstrip-typical
-cp ${APPDIR}/starch/bin/starchstrip-megarow ${OSXPKGDIR}/starchstrip-megarow
-cp ${APPDIR}/starch/bin/starchstrip-float128 ${OSXPKGDIR}/starchstrip-float128
-cp ${APPDIR}/starch/bin/starchcluster_sge-typical ${OSXPKGDIR}/starchcluster_sge-typical
-cp ${APPDIR}/starch/bin/starchcluster_sge-megarow ${OSXPKGDIR}/starchcluster_sge-megarow
-cp ${APPDIR}/starch/bin/starchcluster_sge-float128 ${OSXPKGDIR}/starchcluster_sge-float128
-cp ${APPDIR}/starch/bin/starchcluster_gnuParallel-typical ${OSXPKGDIR}/starchcluster_gnuParallel-typical
-cp ${APPDIR}/starch/bin/starchcluster_gnuParallel-megarow ${OSXPKGDIR}/starchcluster_gnuParallel-megarow
-cp ${APPDIR}/starch/bin/starchcluster_gnuParallel-float128 ${OSXPKGDIR}/starchcluster_gnuParallel-float128
-cp ${APPDIR}/starch/bin/starchcluster_slurm-typical ${OSXPKGDIR}/starchcluster_slurm-typical
-cp ${APPDIR}/starch/bin/starchcluster_slurm-megarow ${OSXPKGDIR}/starchcluster_slurm-megarow
-cp ${APPDIR}/starch/bin/starchcluster_slurm-float128 ${OSXPKGDIR}/starchcluster_slurm-float128
-cp ${APPDIR}/starch/bin/starch-diff-typical ${OSXPKGDIR}/starch-diff-typical
-cp ${APPDIR}/starch/bin/starch-diff-megarow ${OSXPKGDIR}/starch-diff-megarow
-cp ${APPDIR}/starch/bin/starch-diff-float128 ${OSXPKGDIR}/starch-diff-float128
-cp ${APPDIR}/conversion/bin/convert2bed-typical ${OSXPKGDIR}/convert2bed-typical
-cp ${APPDIR}/conversion/bin/convert2bed-megarow ${OSXPKGDIR}/convert2bed-megarow
-cp ${APPDIR}/conversion/bin/convert2bed-float128 ${OSXPKGDIR}/convert2bed-float128
-cp ${APPDIR}/conversion/src/wrappers/bam2bed ${OSXPKGDIR}/bam2bed
-cp ${APPDIR}/conversion/src/wrappers/gff2bed ${OSXPKGDIR}/gff2bed
-cp ${APPDIR}/conversion/src/wrappers/gtf2bed ${OSXPKGDIR}/gtf2bed
......@@ -351,24 +330,8 @@ install_osx_packaging_bins: prep_c all
-cp ${APPDIR}/conversion/src/wrappers/bam2starch_gnuParallel ${OSXPKGDIR}/bam2starch_gnuParallel
-cp ${OTHERDIR}/switch-BEDOPS-binary-type ${OSXPKGDIR}
-cd ${OSXPKGDIR}; \
ln -sf ./sort-bed-typical ./sort-bed; \
ln -sf ./update-sort-bed-slurm-typical ./update-sort-bed-slurm; \
ln -sf ./update-sort-bed-starch-slurm-typical ./update-sort-bed-starch-slurm; \
ln -sf ./update-sort-bed-migrate-candidates-typical ./update-sort-bed-migrate-candidates; \
ln -sf ./bedops-typical ./bedops; \
ln -sf ./closest-features-typical ./closest-features; \
ln -sf ./bedmap-typical ./bedmap; \
ln -sf ./bedextract-typical ./bedextract; \
ln -sf ./starch-typical ./starch; \
ln -sf ./unstarch-typical ./unstarch; \
ln -sf ./starchcat-typical ./starchcat; \
ln -sf ./starchstrip-typical ./starchstrip; \
ln -sf ./starchcluster_sge-typical ./starchcluster_sge; \
ln -sf ./starchcluster_gnuParallel-typical ./starchcluster_gnuParallel; \
ln -sf ./starchcluster_slurm-typical ./starchcluster_slurm; \
ln -sf ./starch-diff-typical ./starch-diff; \
ln -sf ./convert2bed-typical ./convert2bed; \
cd ${CWD}; \
./switch-BEDOPS-binary-type --typical
-cd ${CWD}; \
mkdir -p ${OSXLIBDIR}; \
update_bedops_version:
......@@ -420,6 +383,19 @@ else
find docs/content -type f -exec sed -i "s/"$$OLD_VER"/"$$NEW_VER"/g" {} +
endif
update_bedops_copyright_date:
ifndef OLD_CPD
$(error Old copyright date variable OLD_CPD is undefined (e.g., 2011-2017))
endif
ifndef NEW_CPD
$(error New copyright date variable NEW_CPD is undefined (e.g., 2011-2018))
endif
ifeq ($(KERNEL), Darwin)
gfind . -exec gsed -i "s/"$$OLD_CPD"/"$$NEW_CPD"/g" {} \;
else
find . -exec sed -i "s/"$$OLD_CPD"/"$$NEW_CPD"/g" {} \;
endif
docker: packaging/docker/Dockerfile
docker build -t bedops -f packaging/docker/Dockerfile .
......
README.md
View file @ d20fe563
## BEDOPS v2.4.28: high-performance genomic feature operations ##
## BEDOPS v2.4.32: high-performance genomic feature operations ##
[![Build Status](https://travis-ci.org/bedops/bedops.svg?branch=master)](https://travis-ci.org/bedops/bedops) [![GitHub stars](https://img.shields.io/github/stars/bedops/bedops.svg)](https://github.com/bedops/bedops/stargazers) [![Project license](https://img.shields.io/badge/license-GPLv2-blue.svg)](https://github.com/bedops/bedops/blob/master/LICENSE) [![Documentation Status](https://readthedocs.org/projects/bedops/badge/?version=latest)](https://readthedocs.org/projects/bedops/?badge=latest)
......@@ -6,9 +6,9 @@
### About ###
**BEDOPS v2.4.28** is a suite of tools to address common questions raised in genomic studies — mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data.
**BEDOPS v2.4.32** is a suite of tools to address common questions raised in genomic studies — mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data.
The <a href="https://bedops.readthedocs.io/en/latest/content/overview.html#overview">overview</a> section of the **BEDOPS v2.4.28** documentation summarizes the toolkit, functionality and performance enhancements. The <a href="https://bedops.readthedocs.io/en/latest/index.html#reference">reference</a> table offers documentation for all applications and scripts.
The <a href="https://bedops.readthedocs.io/en/latest/content/overview.html#overview">overview</a> section of the **BEDOPS v2.4.32** documentation summarizes the toolkit, functionality and performance enhancements. The <a href="https://bedops.readthedocs.io/en/latest/index.html#reference">reference</a> table offers documentation for all applications and scripts.
### Downloads ###
......@@ -28,20 +28,20 @@ The <a href="https://bedops.readthedocs.io/en/latest/content/overview.html#overv
<tr>
<td valign="top">
<ul style="list-style-type:square; font-size:smaller; margin-left:0; margin-right:0px; padding-right:0px; padding-left:20px;">
<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.28/bedops_linux_x86_64-v2.4.28.tar.bz2">x86-64 (64-bit)</a> binaries</li>
<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.32/bedops_linux_x86_64-v2.4.32.tar.bz2">x86-64 (64-bit)</a> binaries</li>
<li><a href="http://bedops.readthedocs.io/en/latest/content/installation.html#linux">Installation instructions</a> for Linux hosts</li>
</ul>
</td>
<td valign="top">
<ul style="list-style-type:square; font-size:smaller; margin-left:0; margin-right:0px; padding-right:0px; padding-left:20px;">
<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.28/BEDOPS.2.4.28.pkg.zip">Intel (64-bit, 10.10-10.12)</a> installer package</li>
<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.32/BEDOPS.2.4.32.pkg.zip">Intel (64-bit, 10.10-10.13)</a> installer package</li>
<li><a href="http://bedops.readthedocs.io/en/latest/content/installation.html#mac-os-x">Installation instructions</a> for Mac OS X hosts</li>
</ul>
</td>
<td valign="top">
<ul style="list-style-type:square; font-size:smaller; margin-left:0; margin-right:0px; padding-right:0px; padding-left:20px;">
<li><a href="https://github.com/bedops/bedops/archive/v2.4.28.tar.gz">Source code</a> (tar.gz)</li>
<li><a href="https://github.com/bedops/bedops/archive/v2.4.28.zip">Source code</a> (zip)</li>
<li><a href="https://github.com/bedops/bedops/archive/v2.4.32.tar.gz">Source code</a> (tar.gz)</li>
<li><a href="https://github.com/bedops/bedops/archive/v2.4.32.zip">Source code</a> (zip)</li>
<li><a href="http://bedops.readthedocs.io/en/latest/content/installation.html#installation-via-source-code">Compilation instructions</a></li>
</ul>
</td>
......@@ -50,11 +50,11 @@ The <a href="https://bedops.readthedocs.io/en/latest/content/overview.html#overv
### Documentation ###
Complete documentation for **BEDOPS v2.4.28** tools is available at: <a href="https://bedops.readthedocs.io/en/latest/index.html">https://bedops.readthedocs.io/</a>
Complete documentation for **BEDOPS v2.4.32** tools is available at: <a href="https://bedops.readthedocs.io/en/latest/index.html">https://bedops.readthedocs.io/</a>
### Citation ###
If you use **BEDOPS v2.4.28** in your research, please cite the following manuscript:
If you use **BEDOPS v2.4.32** in your research, please cite the following manuscript:
> Shane Neph, M. Scott Kuehn, Alex P. Reynolds, et al.
> [**BEDOPS: high-performance genomic feature operations**
......@@ -62,7 +62,7 @@ If you use **BEDOPS v2.4.28** in your research, please cite the following manusc
### Copyright ###
> Copyright (C) 2011-2017 Shane J. Neph, M. Scott Kuehn and Alex P. Reynolds
> Copyright (C) 2011-2018 Shane J. Neph, M. Scott Kuehn and Alex P. Reynolds
>
> Source code, documentation and media assets released under <a href="https://github.com/bedops/bedops/blob/master/LICENSE">GNU Public License Version 2</a> (GPL v2).
applications/bed/bedextract/src/ExtractRows.cpp
View file @ d20fe563
......@@ -4,7 +4,7 @@
*/
//
// BEDOPS
// Copyright (C) 2011-2017 Shane Neph, Scott Kuehn and Alex Reynolds
// Copyright (C) 2011-2018 Shane Neph, Scott Kuehn and Alex Reynolds
//
// This program is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
......@@ -49,20 +49,10 @@ namespace {
const std::string prognm = "bedextract";
const std::string citation = BEDOPS::citation();
const std::string version = BEDOPS::revision();
const std::string version = BEDOPS::version();
const std::string authors = "Shane Neph & Alex Reynolds";
constexpr std::size_t PoolSz = 2*8;
#if BEDOPS_BINARY_TYPE == 0
const std::string application_type = "typical";
#else
#if BEDOPS_BINARY_TYPE == 1
const std::string application_type = "megarow";
#else
const std::string application_type = "typical";
#endif
#endif
//======
// Help
//======
......@@ -348,20 +338,20 @@ int main(int argc, char** argv) {
} catch(const Help& h) {
std::cout << prognm << std::endl;
std::cout << " citation: " + citation << std::endl;
std::cout << " version: " + version + " (" + application_type + ")" << std::endl;
std::cout << " version: " + version << std::endl;
std::cout << " authors: " + authors << std::endl;
std::cout << usage() << std::endl;
isok = true;
} catch(const Version& v) {
std::cout << prognm << std::endl;
std::cout << " citation: " + citation << std::endl;
std::cout << " version: " + version + " (" + application_type + ")" << std::endl;
std::cout << " version: " + version << std::endl;
std::cout << " authors: " + authors << std::endl;
isok = true;
} catch(std::string& msg) {
std::cerr << prognm << std::endl;
std::cerr << " citation: " + citation << std::endl;
std::cerr << " version: " + version + " (" + application_type + ")" << std::endl;
std::cerr << " version: " + version << std::endl;
std::cerr << " authors: " + authors << std::endl;
std::cerr << usage() << std::endl;
std::cerr << msg << std::endl;
......
applications/bed/bedextract/src/Makefile
View file @ d20fe563
......@@ -27,17 +27,11 @@ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
BLDFLAGS = -Wall -pedantic -O3 -std=c++11
SFLAGS = -static ${MEGAFLAGS}
ifeq ($(BINARY_TYPE),)
TFLAG = -DBEDOPS_BINARY_TYPE=0
else
TFLAG = -DBEDOPS_BINARY_TYPE=$(BINARY_TYPE_NUM)
endif
dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
dependencies = $(addprefix $(OBJDIR)/, $(addsuffix .o, $(dependency_names)))
FLAGS = $(SFLAGS) -s $(TFLAG) $(BLDFLAGS) $(dependencies) ${LIBLOCATION} ${INCLUDES}
DFLAGS = $(SFLAGS) -g -O0 -std=c++11 -Wall -fno-inline -pedantic $(dependencies) $(TFLAG) ${LIBLOCATION} ${INCLUDES}
GPROFFLAGS = $(SFLAGS) -O -std=c++11 -Wall -pedantic -pg $(dependencies) $(TFLAG) ${LIBLOCATION} ${INCLUDES}
FLAGS = $(SFLAGS) -s $(BLDFLAGS) $(dependencies) ${LIBLOCATION} ${INCLUDES}
DFLAGS = $(SFLAGS) -g -O0 -std=c++11 -Wall -fno-inline -pedantic $(dependencies) ${LIBLOCATION} ${INCLUDES}
GPROFFLAGS = $(SFLAGS) -O -std=c++11 -Wall -pedantic -pg $(dependencies) ${LIBLOCATION} ${INCLUDES}
SOURCE1 = ExtractRows.cpp
BINDIR = ../bin
......
applications/bed/bedextract/src/Makefile.darwin
View file @ d20fe563
......@@ -28,17 +28,11 @@ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++
BLDFLAGS = -O3 ${STDFLAGS}
ifeq ($(BINARY_TYPE),)
TFLAG = -DBEDOPS_BINARY_TYPE=0
else
TFLAG = -DBEDOPS_BINARY_TYPE=$(BINARY_TYPE_NUM)
endif
FLAGS = $(BLDFLAGS) $(MEGAFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
FLAGS = $(BLDFLAGS) $(TFLAG) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
DFLAGS = -g -O0 ${STDFLAGS} $(MEGAFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
DFLAGS = -g -O0 ${STDFLAGS} $(TFLAG) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
GPROFFLAGS = -O -pg ${STDFLAGS} $(TFLAG) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
GPROFFLAGS = -O -pg ${STDFLAGS} $(MEGAFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
SOURCE1 = ExtractRows.cpp
BINDIR = ../bin
......
applications/bed/bedmap/src/Bedmap.cpp
View file @ d20fe563
......@@ -4,7 +4,7 @@
*/
//
// BEDOPS
// Copyright (C) 2011-2017 Shane Neph, Scott Kuehn and Alex Reynolds
// Copyright (C) 2011-2018 Shane Neph, Scott Kuehn and Alex Reynolds
//
// This program is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
......@@ -55,22 +55,12 @@
namespace BedMap {
const std::string prognm = "bedmap";
const std::string version = BEDOPS::revision();
const std::string version = BEDOPS::version();
const std::string authors = "Shane Neph & Scott Kuehn";
const std::string citation = BEDOPS::citation();
constexpr std::size_t PoolSz = 8*8*8;
bool minimumMemory = false;
#if BEDOPS_BINARY_TYPE == 0
const std::string application_type = "typical";
#else
#if BEDOPS_BINARY_TYPE == 1
const std::string application_type = "megarow";
#else
const std::string application_type = "typical";
#endif
#endif
//======
// Help
//======
......@@ -88,6 +78,7 @@ namespace BedMap {
int minRefFields,
int minMapFields,
bool errorCheck,
bool nestCheck,
const std::string& colSep,
const std::string& multivalColSep,
int precision,
......@@ -125,55 +116,57 @@ int main(int argc, char **argv) {
// if all Starch inputs and no nested elements, then can use --faster if the
// overlap criterion allows it.
const bool starchFast = !BedMap::checkStarchNesting(input.refFileName_, input.mapFileName_);
const bool nestCheck = input.errorCheck_ && input.fastMode_;
if ( input.isPercMap_ ) { // % overlap relative to MapType's size (signalmapish)
Bed::PercentOverlapMapping bedDist(input.percOvr_);
Bed::Overlapping sweepDist(0); // dist type for sweep different from BedBaseVisitor's
BedMap::selectSweep(sweepDist, bedDist, input.refFileName_, input.mapFileName_,
input.minRefFields_, input.minMapFields_, input.errorCheck_,
input.minRefFields_, input.minMapFields_, input.errorCheck_, nestCheck,
input.outDelim_, input.multiDelim_, prec, sci, input.fastMode_,
input.sweepAll_, input.chrom_, input.skipUnmappedRows_, visitorNames, visitorArgs);
} else if ( input.isPercRef_ ) { // % overlap relative to RefTypes's size (setops -e)
Bed::PercentOverlapReference bedDist(input.percOvr_);
Bed::Overlapping sweepDist(0); // dist type for sweep different from BedBaseVisitor's
BedMap::selectSweep(sweepDist, bedDist, input.refFileName_, input.mapFileName_,
input.minRefFields_, input.minMapFields_, input.errorCheck_,
input.minRefFields_, input.minMapFields_, input.errorCheck_, nestCheck,
input.outDelim_, input.multiDelim_, prec, sci, input.fastMode_,
input.sweepAll_, input.chrom_, input.skipUnmappedRows_, visitorNames, visitorArgs);
} else if ( input.isPercBoth_ ) { // % overlap relative to both MapType's and RefType's sizes
Bed::PercentOverlapBoth bedDist(input.percOvr_);
Bed::Overlapping sweepDist(0); // dist type for sweep different from BedBaseVisitor's
BedMap::selectSweep(sweepDist, bedDist, input.refFileName_, input.mapFileName_,
input.minRefFields_, input.minMapFields_, input.errorCheck_,
input.minRefFields_, input.minMapFields_, input.errorCheck_, nestCheck,
input.outDelim_, input.multiDelim_, prec, sci, input.fastMode_,
input.sweepAll_, input.chrom_, input.skipUnmappedRows_, visitorNames, visitorArgs);
} else if ( input.isExact_ ) { // must be identical coordinates; should work fine with fully-nested elements
Bed::Exact bedDist;
Bed::Overlapping sweepDist(0); // dist type for sweep different from BedBaseVisitor's
const bool fastMode = true;
const bool noNestCheck = false; // safe with fully-nested elements
BedMap::selectSweep(sweepDist, bedDist, input.refFileName_, input.mapFileName_,
input.minRefFields_, input.minMapFields_, input.errorCheck_,
input.minRefFields_, input.minMapFields_, input.errorCheck_, noNestCheck,
input.outDelim_, input.multiDelim_, prec, sci, fastMode,
input.sweepAll_, input.chrom_, input.skipUnmappedRows_, visitorNames, visitorArgs);
} else if ( input.isPercEither_ ) { // % overlap relative to either MapType's or RefType's size
Bed::PercentOverlapEither bedDist(input.percOvr_);
Bed::Overlapping sweepDist(0); // dist type for sweep different from BedBaseVisitor's
BedMap::selectSweep(sweepDist, bedDist, input.refFileName_, input.mapFileName_,
input.minRefFields_, input.minMapFields_, input.errorCheck_,
input.minRefFields_, input.minMapFields_, input.errorCheck_, nestCheck,
input.outDelim_, input.multiDelim_, prec, sci, input.fastMode_,
input.sweepAll_, input.chrom_, input.skipUnmappedRows_, visitorNames, visitorArgs);
} else if ( input.isRangeBP_ ) { // buffer each reference element
Bed::RangedDist bedDist(input.rangeBP_);
Bed::RangedDist sweepDist(input.rangeBP_); // same as bedDist in this case
BedMap::selectSweep(sweepDist, bedDist, input.refFileName_, input.mapFileName_,
input.minRefFields_, input.minMapFields_, input.errorCheck_,
input.minRefFields_, input.minMapFields_, input.errorCheck_, nestCheck,
input.outDelim_, input.multiDelim_, prec, sci, (input.fastMode_ || starchFast),
input.sweepAll_, input.chrom_, input.skipUnmappedRows_, visitorNames, visitorArgs);
} else { // require a certain amount of bp overlap
Bed::Overlapping bedDist(input.overlapBP_);
Bed::Overlapping sweepDist(0); // dist type for sweep different from BedBaseVisitor's
BedMap::selectSweep(sweepDist, bedDist, input.refFileName_, input.mapFileName_,
input.minRefFields_, input.minMapFields_, input.errorCheck_,
input.minRefFields_, input.minMapFields_, input.errorCheck_, nestCheck,
input.outDelim_, input.multiDelim_, prec, sci, (input.fastMode_ || starchFast),
input.sweepAll_, input.chrom_, input.skipUnmappedRows_, visitorNames, visitorArgs);
}
......@@ -182,19 +175,19 @@ int main(int argc, char **argv) {
} catch(const BedMap::Help& h) { // show usage and exit success
std::cout << BedMap::prognm << std::endl;
std::cout << " citation: " << BedMap::citation << std::endl;
std::cout << " version: " << BedMap::version + " (" + BedMap::application_type + ")" << std::endl;
std::cout << " version: " << BedMap::version << std::endl;
std::cout << " authors: " << BedMap::authors << std::endl;
std::cout << BedMap::Usage() << std::endl;
return EXIT_SUCCESS;
} catch(const BedMap::Version& v) { // show version and exit success
std::cout << BedMap::prognm << std::endl;
std::cout << " citation: " << BedMap::citation << std::endl;
std::cout << " version: " << BedMap::version + " (" + BedMap::application_type + ")" << std::endl;
std::cout << " version: " << BedMap::version << std::endl;
std::cout << " authors: " << BedMap::authors << std::endl;
} catch(const BedMap::NoInput& ni) { // show usage and exit failure
std::cerr << BedMap::prognm << std::endl;
std::cerr << " citation: " << BedMap::citation << std::endl;
std::cerr << " version: " << BedMap::version + " (" + BedMap::application_type + ")" << std::endl;
std::cerr << " version: " << BedMap::version << std::endl;
std::cerr << " authors: " << BedMap::authors << std::endl;
std::cerr << BedMap::Usage() << std::endl;
} catch(std::string& s) {
......@@ -765,6 +758,7 @@ namespace BedMap {
int minRefFields,
int minMapFields,
bool errorCheck,
bool nestCheck,
const std::string& colSep,
const std::string& multivalColSep,
int precision,
......@@ -781,7 +775,6 @@ namespace BedMap {
constexpr bool UseMemPool = true;
constexpr bool NoUseMemPool = !UseMemPool;
const bool nestCheck = ProcessMode;
if ( minMapFields < 4 ) { // just need Bed3
if ( !BedMap::minimumMemory ) {
typedef typename SelectBED<3, UseMemPool>::BType RefType;
......@@ -862,6 +855,7 @@ namespace BedMap {
const std::string& refFileName,
int minRefFields,
bool errorCheck,
bool nestCheck,
const std::string& colSep,
const std::string& multivalColSep,
int precision,
......@@ -871,7 +865,6 @@ namespace BedMap {
const std::vector<std::string>& visitorNames,
const std::vector< std::vector<std::string> >& visitorArgs) {
constexpr bool nestCheck = ProcessMode;
constexpr bool UseMemPool = true;
constexpr bool NoUseMemPool = !UseMemPool;
if ( minRefFields < 4 ) { // just need Bed3
......@@ -943,6 +936,7 @@ namespace BedMap {
int minRefFields,
int minMapFields,
bool errorCheck,
bool nestCheck,
const std::string& colSep,
const std::string& multivalColSep,
int precision,
......@@ -961,19 +955,19 @@ namespace BedMap {
if ( mapFileName.empty() ) { // single-file mode
if ( fastMode )
callSweep<SpecialMode>(st, dt, refFileName, minRefFields, errorCheck, colSep, multivalColSep,
callSweep<SpecialMode>(st, dt, refFileName, minRefFields, errorCheck, nestCheck, colSep, multivalColSep,
precision, useScientific, chrom, skipUnmappedRows, visitorNames, visitorArgs);
else
callSweep<GeneralMode>(st, dt, refFileName, minRefFields, errorCheck, colSep, multivalColSep,
callSweep<GeneralMode>(st, dt, refFileName, minRefFields, errorCheck, nestCheck, colSep, multivalColSep,
precision, useScientific, chrom, skipUnmappedRows, visitorNames, visitorArgs);
} else { // dual-file mode
if ( fastMode )
callSweep<SpecialMode>(st, dt, refFileName, mapFileName, minRefFields, minMapFields,
errorCheck, colSep, multivalColSep, precision, useScientific,
errorCheck, nestCheck, colSep, multivalColSep, precision, useScientific,
chrom, skipUnmappedRows, sweepAll, visitorNames, visitorArgs);
else
callSweep<GeneralMode>(st, dt, refFileName, mapFileName, minRefFields, minMapFields,
errorCheck, colSep, multivalColSep, precision, useScientific,
errorCheck, nestCheck, colSep, multivalColSep, precision, useScientific,
chrom, skipUnmappedRows, sweepAll, visitorNames, visitorArgs);
}
}
......
applications/bed/bedmap/src/Input.hpp
View file @ d20fe563
......@@ -4,7 +4,7 @@
*/
//
// BEDOPS
// Copyright (C) 2011-2017 Shane Neph, Scott Kuehn and Alex Reynolds
// Copyright (C) 2011-2018 Shane Neph, Scott Kuehn and Alex Reynolds
//
// This program is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
......
applications/bed/bedmap/src/Makefile
View file @ d20fe563
......@@ -26,17 +26,11 @@ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
BLDFLAGS = -Wall -pedantic -O3 -std=c++11
SFLAGS = -static
ifeq ($(BINARY_TYPE),)
TFLAG = -DBEDOPS_BINARY_TYPE=0
else
TFLAG = -DBEDOPS_BINARY_TYPE=$(BINARY_TYPE_NUM)
endif
dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
dependencies = $(addprefix $(OBJDIR)/, $(addsuffix .o, $(dependency_names)))
FLAGS = ${TFLAG} ${SFLAGS} ${MEGAFLAGS} -s ${BLDFLAGS} $(dependencies) ${LIBLOCATION} ${INCLUDES}
DFLAGS = ${TFLAG} ${SFLAGS} ${MEGAFLAGS} -g -O0 -std=c++11 -DDEBUG=1 -fno-inline -Wall -pedantic $(dependencies) ${LIBLOCATION} ${INCLUDES}
GPROFFLAGS = ${TFLAG} ${SFLAGS} ${MEGAFLAGS} -pg -O -std=c++11 -Wall -pedantic $(dependencies) ${LIBLOCATION} ${INCLUDES}
FLAGS = ${SFLAGS} ${MEGAFLAGS} -s ${BLDFLAGS} $(dependencies) ${LIBLOCATION} ${INCLUDES}
DFLAGS = ${SFLAGS} ${MEGAFLAGS} -g -O0 -std=c++11 -DDEBUG=1 -fno-inline -Wall -pedantic $(dependencies) ${LIBLOCATION} ${INCLUDES}
GPROFFLAGS = ${SFLAGS} ${MEGAFLAGS} -pg -O -std=c++11 -Wall -pedantic $(dependencies) ${LIBLOCATION} ${INCLUDES}
SOURCE1 = Bedmap.cpp
BINDIR = ../bin
......
applications/bed/bedmap/src/Makefile.darwin
View file @ d20fe563
......@@ -28,17 +28,11 @@ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++
BLDFLAGS = -O3 ${STDFLAGS}
ifeq ($(BINARY_TYPE),)
TFLAG = -DBEDOPS_BINARY_TYPE=0
else
TFLAG = -DBEDOPS_BINARY_TYPE=$(BINARY_TYPE_NUM)
endif
FLAGS = $(MEGAFLAGS) $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
FLAGS = $(TFLAG) $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
DFLAGS = -g -O0 -DDEBUG=1 $(MEGAFLAGS) ${STDFLAGS} $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
DFLAGS = -g -O0 -DDEBUG=1 $(TFLAG) ${STDFLAGS} $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
GPROFFLAGS = -O -pg $(TFLAG) ${STDFLAGS} $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
GPROFFLAGS = -O -pg $(MEGAFLAGS) ${STDFLAGS} $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
SOURCE1 = Bedmap.cpp
BINDIR = ../bin
......
applications/bed/bedmap/src/TDefs.hpp
View file @ d20fe563
......@@ -4,7 +4,7 @@
*/
//
// BEDOPS
// Copyright (C) 2011-2017 Shane Neph, Scott Kuehn and Alex Reynolds
// Copyright (C) 2011-2018 Shane Neph, Scott Kuehn and Alex Reynolds
//
// This program is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
......
applications/bed/bedops/src/BedPadReader.hpp
View file @ d20fe563
......@@ -4,7 +4,7 @@
*/
//
// BEDOPS
// Copyright (C) 2011-2017 Shane Neph, Scott Kuehn and Alex Reynolds
// Copyright (C) 2011-2018 Shane Neph, Scott Kuehn and Alex Reynolds
//
// This program is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
......
applications/bed/bedops/src/Bedops.cpp
View file @ d20fe563
......@@ -4,7 +4,7 @@
*/
//
// BEDOPS
// Copyright (C) 2011-2017 Shane Neph, Scott Kuehn and Alex Reynolds
// Copyright (C) 2011-2018 Shane Neph, Scott Kuehn and Alex Reynolds
//
// This program is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
......@@ -106,19 +106,9 @@ namespace BedOperations {
const std::string prognm = "bedops";
const std::string citation = BEDOPS::citation();
const std::string version = BEDOPS::revision();
const std::string version = BEDOPS::version();
const std::string authors = "Shane Neph & Scott Kuehn";
#if BEDOPS_BINARY_TYPE == 0
const std::string application_type = "typical";
#else
#if BEDOPS_BINARY_TYPE == 1
const std::string application_type = "megarow";
#else
const std::string application_type = "typical";
#endif
#endif
void doWork(const Input& input);
} // namespace BedOperations
......@@ -136,7 +126,7 @@ int main(int argc, char** argv) {
} catch(BedOperations::HelpException& h) {
std::cout << BedOperations::prognm << std::endl;
std::cout << " citation: " + BedOperations::citation << std::endl;
std::cout << " version: " + BedOperations::version + " (" + BedOperations::application_type + ")" << std::endl;
std::cout << " version: " + BedOperations::version << std::endl;
std::cout << " authors: " + BedOperations::authors << std::endl;
std::cout << BedOperations::Usage() << std::endl;
return(EXIT_SUCCESS);
......@@ -144,7 +134,7 @@ int main(int argc, char** argv) {
try {
std::cout << BedOperations::prognm << std::endl;
std::cout << " citation: " + BedOperations::citation << std::endl;
std::cout << " version: " + BedOperations::version + " (" + BedOperations::application_type + ")" << std::endl;
std::cout << " version: " + BedOperations::version << std::endl;
std::cout << " authors: " + BedOperations::authors << std::endl;
std::cout << BedOperations::DetailedUsage(e.m_) << std::endl;
} catch(const std::exception& s) {
......@@ -154,13 +144,13 @@ int main(int argc, char** argv) {
} catch(BedOperations::Version& v) {
std::cout << BedOperations::prognm << std::endl;
std::cout << " citation: " + BedOperations::citation << std::endl;
std::cout << " version: " + BedOperations::version + " (" + BedOperations::application_type + ")" << std::endl;
std::cout << " version: " + BedOperations::version << std::endl;
std::cout << " authors: " + BedOperations::authors << std::endl;
return(EXIT_SUCCESS);
} catch(BedOperations::NoInput& ni) {
std::cout << BedOperations::prognm << std::endl;
std::cout << " citation: " + BedOperations::citation << std::endl;
std::cout << " version: " + BedOperations::version + " (" + BedOperations::application_type + ")" << std::endl;
std::cout << " version: " + BedOperations::version << std::endl;
std::cout << " authors: " + BedOperations::authors << std::endl;
std::cerr << BedOperations::Usage() << std::endl;
} catch(std::string& s) {
......
applications/bed/bedops/src/Input.hpp
View file @ d20fe563
......@@ -4,7 +4,7 @@
*/
//
// BEDOPS
// Copyright (C) 2011-2017 Shane Neph, Scott Kuehn and Alex Reynolds
// Copyright (C) 2011-2018 Shane Neph, Scott Kuehn and Alex Reynolds
//
// This program is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
......
applications/bed/bedops/src/Makefile
View file @ d20fe563
......@@ -28,17 +28,11 @@ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
BLDFLAGS = -Wall -pedantic -O3 -std=c++11
SFLAGS = -static
ifeq ($(BINARY_TYPE),)
TFLAG = -DBEDOPS_BINARY_TYPE=0
else
TFLAG = -DBEDOPS_BINARY_TYPE=$(BINARY_TYPE_NUM)
endif
dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
dependencies = $(addprefix $(OBJDIR)/, $(addsuffix .o, $(dependency_names)))
FLAGS = $(SFLAGS) $(TFLAG) ${MEGAFLAGS} -s $(BLDFLAGS) $(dependencies) ${LIBLOCATION} ${INCLUDES}
DFLAGS = $(SFLAGS) $(TFLAG) ${MEGAFLAGS} -g -O0 -DDEBUG_VERBOSE=1 -std=c++11 -Wall -fno-inline -pedantic -DDEBUG=1 $(dependencies) ${LIBLOCATION} ${INCLUDES}
GPROFFLAGS = $(SFLAGS) $(TFLAG) ${MEGAFLAGS} -O -std=c++11 -Wall -pedantic -pg $(dependencies) ${LIBLOCATION} ${INCLUDES}
FLAGS = $(SFLAGS) ${MEGAFLAGS} -s $(BLDFLAGS) $(dependencies) ${LIBLOCATION} ${INCLUDES}
DFLAGS = $(SFLAGS) ${MEGAFLAGS} -g -O0 -DDEBUG_VERBOSE=1 -std=c++11 -Wall -fno-inline -pedantic -DDEBUG=1 $(dependencies) ${LIBLOCATION} ${INCLUDES}
GPROFFLAGS = $(SFLAGS) ${MEGAFLAGS} -O -std=c++11 -Wall -pedantic -pg $(dependencies) ${LIBLOCATION} ${INCLUDES}
SOURCE1 = Bedops.cpp
BINDIR = ../bin
PROG = bedops-${BINARY_TYPE}
......
applications/bed/bedops/src/Makefile.darwin
View file @ d20fe563
......@@ -27,17 +27,11 @@ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++
BLDFLAGS = -O3 ${STDFLAGS}
ifeq ($(BINARY_TYPE),)
TFLAG = -DBEDOPS_BINARY_TYPE=0
else
TFLAG = -DBEDOPS_BINARY_TYPE=$(BINARY_TYPE_NUM)
endif
FLAGS = ${MEGAFLAGS} $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
FLAGS = ${TFLAG} ${MEGAFLAGS} $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
DFLAGS = ${MEGAFLAGS} -g -O0 -DDEBUG_VERBOSE=1 -DDEBUG=1 ${STDFLAGS} $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
DFLAGS = ${TFLAG} ${MEGAFLAGS} -g -O0 -DDEBUG_VERBOSE=1 -DDEBUG=1 ${STDFLAGS} $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
GPROFFLAGS = ${TFLAG} ${MEGAFLAGS} -O -pg ${STDFLAGS} $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
GPROFFLAGS = ${MEGAFLAGS} -O -pg ${STDFLAGS} $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
SOURCE1 = Bedops.cpp
BINDIR = ../bin
......
applications/bed/closestfeats/src/BedReader.hpp
View file @ d20fe563
......@@ -4,7 +4,7 @@
*/
//
// BEDOPS
// Copyright (C) 2011-2017 Shane Neph, Scott Kuehn and Alex Reynolds
// Copyright (C) 2011-2018 Shane Neph, Scott Kuehn and Alex Reynolds
//
// This program is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
......
applications/bed/closestfeats/src/ClosestFeature.cpp
View file @ d20fe563
......@@ -4,7 +4,7 @@
*/
//
// BEDOPS
// Copyright (C) 2011-2017 Shane Neph, Scott Kuehn and Alex Reynolds
// Copyright (C) 2011-2018 Shane Neph, Scott Kuehn and Alex Reynolds
//
// This program is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
......@@ -50,7 +50,7 @@
namespace FeatDist {
const std::string prognm = "closest-features";
const std::string version = BEDOPS::revision();
const std::string version = BEDOPS::version();
const std::string authors = "Shane Neph & Scott Kuehn";
const std::string citation = BEDOPS::citation();
const char* none = "NA";
......@@ -58,16 +58,6 @@ namespace FeatDist {
const Bed::SignedCoordType minus_infinite = std::numeric_limits<Bed::SignedCoordType>::min();
const std::size_t PoolSz = 8*8*8; // only 2 file inputs
#if BEDOPS_BINARY_TYPE == 0
const std::string application_type = "typical";
#else
#if BEDOPS_BINARY_TYPE == 1
const std::string application_type = "megarow";
#else
const std::string application_type = "typical";
#endif
#endif
void doWork(const Input&);
} // namespace FeatDist
......@@ -85,20 +75,20 @@ int main(int argc, char** argv) {
} catch(FeatDist::HelpException& h) {
std::cout << FeatDist::prognm << std::endl;
std::cout << " citation: " + FeatDist::citation << std::endl;
std::cout << " version: " + FeatDist::version + " (" + FeatDist::application_type + ")" << std::endl;
std::cout << " version: " + FeatDist::version << std::endl;
std::cout << " authors: " + FeatDist::authors << std::endl;
std::cout << FeatDist::Usage() << std::endl;
return(EXIT_SUCCESS);
} catch(FeatDist::VersionException& v) {
std::cout << FeatDist::prognm << std::endl;
std::cout << " citation: " + FeatDist::citation << std::endl;
std::cout << " version: " + FeatDist::version + " (" + FeatDist::application_type + ")" << std::endl;
std::cout << " version: " + FeatDist::version << std::endl;
std::cout << " authors: " + FeatDist::authors << std::endl;
return(EXIT_SUCCESS);
} catch(FeatDist::NoInput& ni) {
std::cerr << FeatDist::prognm << std::endl;
std::cerr << " citation: " + FeatDist::citation << std::endl;
std::cerr << " version: " + FeatDist::version + " (" + FeatDist::application_type + ")" << std::endl;
std::cerr << " version: " + FeatDist::version << std::endl;
std::cerr << " authors: " + FeatDist::authors << std::endl;
std::cerr << FeatDist::Usage() << std::endl;
} catch(const std::exception& stx) {
......
applications/bed/closestfeats/src/Input.hpp
View file @ d20fe563
......@@ -4,7 +4,7 @@
*/
//
// BEDOPS
// Copyright (C) 2011-2017 Shane Neph, Scott Kuehn and Alex Reynolds
// Copyright (C) 2011-2018 Shane Neph, Scott Kuehn and Alex Reynolds
//
// This program is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
......
applications/bed/closestfeats/src/Makefile
View file @ d20fe563
......@@ -26,17 +26,11 @@ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
BLDFLAGS = -Wall -pedantic -O3 -std=c++11
SFLAGS = -static
ifeq ($(BINARY_TYPE),)
TFLAG = -DBEDOPS_BINARY_TYPE=0
else
TFLAG = -DBEDOPS_BINARY_TYPE=$(BINARY_TYPE_NUM)
endif
dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
dependencies = $(addprefix $(OBJDIR)/, $(addsuffix .o, $(dependency_names)))
FLAGS = $(SFLAGS) $(TFLAG) ${MEGAFLAGS} -s $(BLDFLAGS) $(dependencies) ${LIBLOCATION} ${INCLUDES}
DFLAGS = $(SFLAGS) $(TFLAG) ${MEGAFLAGS} -g -O0 -std=c++11 -Wall -fno-inline -pedantic $(dependencies) ${LIBLOCATION} ${INCLUDES}
GPROFFLAGS = $(SFLAGS) $(TFLAG) ${MEGAFLAGS} -O -std=c++11 -Wall -pedantic -pg $(dependencies) ${LIBLOCATION} ${INCLUDES}
FLAGS = $(SFLAGS) ${MEGAFLAGS} -s $(BLDFLAGS) $(dependencies) ${LIBLOCATION} ${INCLUDES}
DFLAGS = $(SFLAGS) ${MEGAFLAGS} -g -O0 -std=c++11 -Wall -fno-inline -pedantic $(dependencies) ${LIBLOCATION} ${INCLUDES}
GPROFFLAGS = $(SFLAGS) ${MEGAFLAGS} -O -std=c++11 -Wall -pedantic -pg $(dependencies) ${LIBLOCATION} ${INCLUDES}
SOURCE1 = ClosestFeature.cpp
BINDIR = ../bin
PROG = closest-features-${BINARY_TYPE}
......
applications/bed/closestfeats/src/Makefile.darwin
View file @ d20fe563
......@@ -28,17 +28,11 @@ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++
BLDFLAGS = -O3 ${STDFLAGS}
ifeq ($(BINARY_TYPE),)
TFLAG = -DBEDOPS_BINARY_TYPE=0
else
TFLAG = -DBEDOPS_BINARY_TYPE=$(BINARY_TYPE_NUM)
endif
FLAGS = ${MEGAFLAGS} $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
FLAGS = ${TFLAG} ${MEGAFLAGS} $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
DFLAGS = ${MEGAFLAGS} -g -O0 ${STDFLAGS} $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
DFLAGS = ${TFLAG} ${MEGAFLAGS} -g -O0 ${STDFLAGS} $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
GPROFFLAGS = ${TFLAG} ${MEGAFLAGS} -O -pg ${STDFLAGS} $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
GPROFFLAGS = ${MEGAFLAGS} -O -pg ${STDFLAGS} $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
SOURCE1 = ClosestFeature.cpp
BINDIR = ../bin
......