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comment	@# @;


1.1
date	2025.01.20.17.29.58;	author bacon;	state Exp;
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commitid	Tl3I5DnOJsXzsfGF;


desc
@@


1.1
log
@biology/subread: Alignment, quantification, SNPs

The Subread package comprises a suite of software programs for
processing next-gen sequencing read data including:

    Subread: a general-purpose read aligner which can align both
    genomic DNA-seq and RNA-seq reads. It can also be used to
    discover genomic mutations including short indels and structural
    variants.

    Subjunc: a read aligner developed for aligning RNA-seq reads
    and for the detection of exon-exon junctions. Gene fusion events
    can be detected as well.

    featureCounts: a software program developed for counting
    reads to genomic features such as genes, exons, promoters and
    genomic bins.

    Sublong: a long-read aligner that is designed based on
    seed-and-vote.

    exactSNP: a SNP caller that discovers SNPs by testing signals
    against local background noises.
@
text
@

include makefile.version

CCFLAGS = -DMAKE_FOR_EXON  -DMAKE_STANDALONE \
	-DSUBREAD_VERSION=\"${SUBREAD_VERSION}\"  -D_FILE_OFFSET_BITS=64
LDFLAGS += -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lz -lm
CC ?= gcc
CC += ${CCFLAGS}

BINS	= detectionCall sublong repair txUnique featureCounts removeDup \
	exactSNP subread-buildindex subindel  subread-align subjunc \
	qualityScores subread-fullscan propmapped flattenGTF \

MKDIR	?= mkdir -p
INSTALL	?= install
DESTDIR	?= .
PREFIX	?= local
STRIP	?= strip

ALL_LIBS= core core-junction core-indel sambam-file sublog gene-algorithms hashtable input-files sorted-hashtable gene-value-index exon-algorithms HelperFunctions interval_merge long-hashtable core-bigtable seek-zlib input-blc
ALL_OBJECTS=$(addsuffix .o, ${ALL_LIBS})
ALL_H=$(addsuffix .h, ${ALL_LIBS})
ALL_C=$(addsuffix .c, ${ALL_LIBS})

all: genRandomReads detectionCall sublong repair txUnique featureCounts removeDup exactSNP subread-buildindex subindel  subread-align subjunc qualityScores subread-fullscan propmapped flattenGTF # samMappedBases mergeVCF  testZlib
	mkdir -p ../bin/utilities
	mv longread-one/LRM longread-one/sublong
	mv longread-one/sublong subread-align subjunc featureCounts  subindel exactSNP subread-buildindex ../bin/
	mv detectionCall genRandomReads repair propmapped qualityScores removeDup subread-fullscan txUnique flattenGTF ../bin/utilities

sublong: longread-one/longread-mapping.c  ${ALL_OBJECTS}
	echo " " > longread-one/make.version
	rm -f longread-one/*.o
	cd longread-one && $(MAKE)

genRandomReads: gen_rand_reads.c ${ALL_OBJECTS}
	${CC} -o genRandomReads gen_rand_reads.c ${ALL_OBJECTS} ${LDFLAGS}

flattenGTF: flattenAnnotations.c ${ALL_OBJECTS}
	${CC} -o flattenGTF flattenAnnotations.c  ${ALL_OBJECTS} ${LDFLAGS}

detectionCall: detection-calls.c	 ${ALL_OBJECTS}
	${CC} -o detectionCall detection-calls.c  ${ALL_OBJECTS} ${LDFLAGS}

repair: read-repair.c	 ${ALL_OBJECTS}
	${CC} -o repair read-repair.c  ${ALL_OBJECTS} ${LDFLAGS}

txUnique: tx-unique.c tx-unique.h	 ${ALL_OBJECTS}
	${CC} -o txUnique tx-unique.c  ${ALL_OBJECTS} ${LDFLAGS}

globalReassembly: global-reassembly.c ${ALL_OBJECTS}
	${CC} -o globalReassembly  global-reassembly.c ${ALL_OBJECTS} ${LDFLAGS}

propmapped: propmapped.c ${ALL_OBJECTS}
	${CC} -o propmapped propmapped.c ${ALL_OBJECTS} ${LDFLAGS}

exactSNP: SNPCalling.c SNPCalling.h  ${ALL_OBJECTS}
	${CC}  -o exactSNP SNPCalling.c  ${ALL_OBJECTS} ${LDFLAGS}

subread-buildindex: index-builder.c subread.h ${ALL_OBJECTS}
	${CC}  -o subread-buildindex  index-builder.c ${ALL_OBJECTS} ${LDFLAGS}

removeDup: removeDupReads.c removeDupReads.h subread.h ${ALL_OBJECTS}
	${CC} -o  removeDup removeDupReads.c  ${ALL_OBJECTS} ${LDFLAGS}

subindel: SUBindel.c core.h subread.h  ${ALL_OBJECTS}
	${CC} -o subindel SUBindel.c ${ALL_OBJECTS} ${LDFLAGS}

featureCounts: readSummary.c subread.h  ${ALL_OBJECTS}
	${CC} -o featureCounts readSummary.c ${ALL_OBJECTS} ${LDFLAGS}

subread-align: core-interface-aligner.c  ${ALL_OBJECTS}
	${CC} -o subread-align core-interface-aligner.c  ${ALL_OBJECTS} ${LDFLAGS} 

subjunc: core-interface-subjunc.c  ${ALL_OBJECTS}
	${CC} -o subjunc core-interface-subjunc.c  ${ALL_OBJECTS} ${LDFLAGS} 

subtools: subtools.c ${ALL_OBJECTS}
	${CC} -o subtools subtools.c ${ALL_OBJECTS} ${LDFLAGS} 

qualityScores: qualityScores.c ${ALL_OBJECTS}
	${CC} -o qualityScores qualityScores.c  ${ALL_OBJECTS}  ${LDFLAGS}

subread-fullscan: fullscan.c  ${ALL_OBJECTS}
	${CC} -o subread-fullscan fullscan.c  ${ALL_OBJECTS}  ${LDFLAGS}

.PHONY:	clean install install-strip

install-strip: install
	${STRIP} ${DESTDIR}${PREFIX}/bin/*

install:
	${MKDIR} ${DESTDIR}${PREFIX}/bin
	${INSTALL} -c \
		../bin/exactSNP \
		../bin/featureCounts \
		../bin/sub* \
		../bin/utilities/* \
		${DESTDIR}${PREFIX}/bin

clean:
	rm -f core featureCounts exactSNP removeDup subread-buildindex \
		${ALL_OBJECTS}
@