New upstream version 1.6.2+dfsg (b354f0db) · Commits · Debian Med / subread

doc/SubreadUsersGuide.tex

+79 −66

File changed.

Preview size limit exceeded, changes collapsed.

src/HelperFunctions.c

+14 −0

Original line number	Diff line number	Diff line
		@@ -52,6 +52,20 @@
		#include "HelperFunctions.h"


		char * get_short_fname(char * lname){
		char * ret = lname;

		int x1;
		for(x1 = strlen(lname)-1; x1>=0; x1--){
		if(lname [x1] == '/'){
		ret = lname + x1 + 1;
		break;
		}
		}
		return ret;
		}



		// This assumes the first part of Cigar has differet strandness to the main part of the cigar.
		// Pos is the LAST WANTED BASE location before the first strand jump (split by 'b' or 'n').

src/HelperFunctions.h

+2 −0

Original line number	Diff line number	Diff line
		@@ -75,4 +75,6 @@ int load_features_annotation(char * file_name, int file_type, char * gene_id_col
		void * context, int do_add_feature(char * gene_name, char * transcript_id, char * chrome_name, unsigned int start, unsigned int end, int is_negative_strand, void * context) );

		HashTable * load_alias_table(char * fname) ;

		char * get_short_fname(char * lname);
		#endif

src/Makefile.Linux

+11 −5

Original line number	Diff line number	Diff line
		#MACOS = -D MACOS

		include makefile.version

		CC_EXEC = gcc
		OPT_LEVEL = 3
		CCFLAGS = -mtune=core2 ${MACOS} -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\" -D_FILE_OFFSET_BITS=64 # -w

		include makefile.version
		-include ~/.R/DBPZ_debug_makefile

		CCFLAGS = -mtune=core2 ${MACOS} -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\" -D_FILE_OFFSET_BITS=64 ${WARNING_LEVEL}
		LDFLAGS = ${STATIC_MAKE} -pthread -lz -lm ${MACOS} -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE
		CC_EXEC = gcc
		CC = ${CC_EXEC} ${CCFLAGS} -fmessage-length=0 -ggdb


		@@ -14,11 +17,11 @@ ALL_OBJECTS=$(addsuffix .o, ${ALL_LIBS})
		ALL_H=$(addsuffix .h, ${ALL_LIBS})
		ALL_C=$(addsuffix .c, ${ALL_LIBS})

		all: detectionCall sublong repair txUnique featureCounts removeDup exactSNP subread-buildindex subindel subread-align subjunc qualityScores subread-fullscan propmapped coverageCount # samMappedBases mergeVCF testZlib
		all: detectionCall sublong repair txUnique featureCounts removeDup exactSNP subread-buildindex subindel subread-align subjunc qualityScores subread-fullscan propmapped coverageCount 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 repair coverageCount propmapped qualityScores removeDup subread-fullscan txUnique ../bin/utilities
		mv detectionCall repair coverageCount propmapped qualityScores removeDup subread-fullscan txUnique flattenGTF ../bin/utilities
		@echo
		@echo "###########################################################"
		@echo "# #"
		@@ -34,6 +37,9 @@ sublong: longread-one/longread-mapping.c ${ALL_OBJECTS}
		rm -f longread-one/*.o
		cd longread-one && $(MAKE)

		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}

src/Makefile.MacOS

+6 −3

Original line number	Diff line number	Diff line
		MACOS = -D MACOS
		include makefile.version

		CCFLAGS = -mtune=core2 ${MACOS} -O9 -w -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\" -D_FILE_OFFSET_BITS=64
		CCFLAGS = -mtune=core2 ${MACOS} -O9 -w -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\" -D_FILE_OFFSET_BITS=64 ${WARNING_LEVEL}
		LDFLAGS = -pthread -lz -lm ${MACOS} -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST
		CC = gcc ${CCFLAGS} ${STATIC_MAKE} -ggdb -fomit-frame-pointer -O3 -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fmessage-length=0

		@@ -11,11 +11,11 @@ ALL_OBJECTS=$(addsuffix .o, ${ALL_LIBS})
		ALL_H=$(addsuffix .h, ${ALL_LIBS})
		ALL_C=$(addsuffix .c, ${ALL_LIBS})

		all: sublong repair featureCounts removeDup exactSNP subread-buildindex subindel subread-align subjunc qualityScores subread-fullscan propmapped coverageCount # globalReassembly testZlib
		all: sublong repair featureCounts removeDup exactSNP subread-buildindex subindel subread-align subjunc qualityScores subread-fullscan propmapped coverageCount flattenGTF # globalReassembly 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 repair coverageCount subread-fullscan qualityScores removeDup propmapped ../bin/utilities
		mv repair coverageCount subread-fullscan qualityScores removeDup propmapped flattenGTF ../bin/utilities
		@echo
		@echo "###########################################################"
		@echo "# #"
		@@ -31,6 +31,9 @@ sublong: longread-one/longread-mapping.c ${ALL_OBJECTS}
		rm -f longread-one/*.o
		cd longread-one && $(MAKE)

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

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