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Makefile
View file @ f18dccae
CC?=gcc
LD=${CC}
CFLAGS= -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools
CFLAGS += -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools
CFLAGS += `pkg-config --cflags htslib`
INC := -I include
CTAGS = ctags > tags
LIB = -lm -lpthread -lz -lncurses -L libs -lform -lmenu -L/usr/local/lib/
LIB += -lm -lpthread -lz -lncurses -L libs -lform -lmenu -L/usr/local/lib/
LIB += `pkg-config --libs htslib`
LIB += "-Wl,-rpath,`pkg-config --variable=libdir htslib`"
......@@ -30,7 +30,7 @@ LIBOBJECTS := $(patsubst $(LIBDIR)/%,$(BUILDDIR)/%,$(LIBSOURCES:.$(SRCEXT)=.o))
$(PRGTARGETS): $(OBJECTS)
@echo "Linking $@";
$(LD) $(LIBOBJECTS) $(BUILDDIR)/$@.o -o $(TARGETDIR)/$@$(TARGETEXT) $(LIB)
$(LD) $(LIBOBJECTS) $(BUILDDIR)/$@.o -o $(TARGETDIR)/$@$(TARGETEXT) $(LIB) $(LDFLAGS)
$(BUILDDIR)/%.o: $(LIBDIR)/%.c
......
Makefile.bak
View file @ f18dccae
CC?=gcc
LD=${CC}
CFLAGS= -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools
CFLAGS += -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools
CFLAGS += `pkg-config --cflags htslib`
INC := -I include
CTAGS = ctags > tags
LIB = -lm -lpthread -lz -lncurses -L libs -lform -lmenu -L/usr/local/lib/
LIB += -lm -lpthread -lz -lncurses -L libs -lform -lmenu -L/usr/local/lib/
LIB += `pkg-config --libs htslib`
LIB += "-Wl,-rpath,`pkg-config --variable=libdir htslib`"
......@@ -30,7 +30,7 @@ LIBOBJECTS := $(patsubst $(LIBDIR)/%,$(BUILDDIR)/%,$(LIBSOURCES:.$(SRCEXT)=.o))
$(PRGTARGETS): $(OBJECTS)
@echo "Linking $@";
$(LD) $(LIBOBJECTS) $(BUILDDIR)/$@.o -o $(TARGETDIR)/$@$(TARGETEXT) $(LIB)
$(LD) $(LIBOBJECTS) $(BUILDDIR)/$@.o -o $(TARGETDIR)/$@$(TARGETEXT) $(LIB) $(LDFLAGS)
$(BUILDDIR)/%.o: $(LIBDIR)/%.c
......
debian/changelog
View file @ f18dccae
segemehl (0.3.2-1) unstable; urgency=medium
* Fix watch file
* New upstream version
-- Andreas Tille <tille@debian.org> Tue, 04 Dec 2018 15:51:18 +0100
segemehl (0.3-1) unstable; urgency=medium
* Initial release (Closes: #910357)
......
debian/patches/hardening.patch deleted 100644 → 0
View file @ a5cd9d2d
Author: Andreas Tille <tille@debian.org>
Last-Update: Fri, 05 Oct 2018 09:54:55 +0200
Description: Propagate hardening options
--- a/Makefile
+++ b/Makefile
@@ -1,10 +1,10 @@
CC?=gcc
LD=${CC}
-CFLAGS= -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools
+CFLAGS += -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools
CFLAGS += `pkg-config --cflags htslib`
INC := -I include
CTAGS = ctags > tags
-LIB = -lm -lpthread -lz -lncurses -L libs -lform -lmenu -L/usr/local/lib/
+LIB += -lm -lpthread -lz -lncurses -L libs -lform -lmenu -L/usr/local/lib/
LIB += `pkg-config --libs htslib`
LIB += "-Wl,-rpath,`pkg-config --variable=libdir htslib`"
@@ -30,7 +30,7 @@ LIBOBJECTS := $(patsubst $(LIBDIR)/%,$(
$(PRGTARGETS): $(OBJECTS)
@echo "Linking $@";
- $(LD) $(LIBOBJECTS) $(BUILDDIR)/$@.o -o $(TARGETDIR)/$@$(TARGETEXT) $(LIB)
+ $(LD) $(LIBOBJECTS) $(BUILDDIR)/$@.o -o $(TARGETDIR)/$@$(TARGETEXT) $(LIB) $(LDFLAGS)
$(BUILDDIR)/%.o: $(LIBDIR)/%.c
debian/patches/series
View file @ f18dccae
hardening.patch
rpath.patch
spelling.patch
debian/patches/spelling.patch deleted 100644 → 0
View file @ a5cd9d2d
Author: Andreas Tille <tille@debian.org>
Last-Update: Fri, 05 Oct 2018 09:54:55 +0200
Description: Fix spelling
--- a/libs/biofiles.c
+++ b/libs/biofiles.c
@@ -1586,7 +1586,7 @@ bl_fastxAddMate(void *space,
if(bl_fastaCheckMateID(f, n, descr, descrlen) == 0) {
NFO("The fasta/fastq IDs in both mate files do not match.\n", NULL);
- NFO("The first mismatch occured at fastq number %u\n", n);
+ NFO("The first mismatch occurred at fastq number %u\n", n);
NFO("Exiting.\n", NULL);
exit(EXIT_FAILURE);
}
@@ -3448,7 +3448,7 @@ bl_annotationRead (void *space, char *fn
} else if(!strcmp(suf, ".gff") || !strcmp(suf, ".gff3")) {
annot = bl_GFFread(NULL, fn);
} else {
- NFO("please provide a bed or gff file with the approriate extension.\n", NULL);
+ NFO("please provide a bed or gff file with the appropriate extension.\n", NULL);
exit(EXIT_FAILURE);
}
return annot;
--- a/libs/gzidx.c
+++ b/libs/gzidx.c
@@ -554,7 +554,7 @@ int bl_bgzFillStream(FILE *fp, unsigned
n = fread(&input[strm->avail_in], 1, CHUNK-strm->avail_in, fp);
if (ferror(fp)) {
fprintf(stderr, "error reading bgz file.\n");
- perror("The following error occured:");
+ perror("The following error occurred:");
exit(EXIT_FAILURE);
}
--- a/libs/haarz.c
+++ b/libs/haarz.c
@@ -413,7 +413,7 @@ int main(int argc,char** argv) {
prg = manopt_getopts(&prgset, MIN(argc,2), argv);
if(prg->noofvalues == 1) {
- manopt_help(&prgset, "programm needs to be selected\n");
+ manopt_help(&prgset, "program needs to be selected\n");
}
manopt_initoptionset(&optset, argv[0], NULL,
@@ -848,7 +848,7 @@ int main(int argc,char** argv) {
FREEMEMORY(NULL, unflagged);
} else {
- manopt_help(&prgset, "unkown program selected\n");
+ manopt_help(&prgset, "unknown program selected\n");
}
manopt_destructoptionset(&optset);
--- a/libs/manopt.c
+++ b/libs/manopt.c
@@ -1039,7 +1039,7 @@ manopt_checkconstraint(manopt_optionset*
case MANOPT_BLOCKSEPARATOR:
break;
default:
- manopt_help(optset, "unkown option %s type\n", argset->args[arg].flagname);
+ manopt_help(optset, "unknown option %s type\n", argset->args[arg].flagname);
break;
}
--- a/libs/multicharseq.c
+++ b/libs/multicharseq.c
@@ -423,7 +423,7 @@ initMultiCharSeqAlignment(
a->refstart = MAX(sub_start, (Lint)pos-loff);
if(a->refstart > sub_end) {
- fprintf(stderr, "refstart > substart: skiping MultiCharSeqAlignment\n");
+ fprintf(stderr, "refstart > substart: skipping MultiCharSeqAlignment\n");
return 0;
}
@@ -480,7 +480,7 @@ initMultiCharSeqAlignmentOpt(
//this should not happen
if(a->refstart > sub_end) {
- fprintf(stderr, "refstart > substart: skiping MultiCharSeqAlignment\n");
+ fprintf(stderr, "refstart > substart: skipping MultiCharSeqAlignment\n");
return 0;
}
debian/watch
View file @ f18dccae
version=4
opts="uversionmangle=s/_/./g,repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
http://www.bioinf.uni-leipzig.de/Software/segemehl/ .*/segemehl_(\d[_.\d]+)\.tar\.gz
http://www.bioinf.uni-leipzig.de/Software/segemehl/ .*/segemehl@ANY_VERSION@@ARCHIVE_EXT@
# opts="searchmode=plain,uversionmangle=s/_/./g,repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
# May be we can use searchmode=plain to fetch "<a href="downloads/segemehl.tar.gz">Download segemehl version 0.3</a>"
......
include/version.h
View file @ f18dccae
......@@ -24,11 +24,11 @@
#define VERSION "v0.3.0"
#define VERSION "0.3.2"
#define REVISION "g0690723"
#define REVISION "g664b3dd"
#define TIME "2018-10-02 21:03:46 +0200"
#define TIME "2018-11-11 17:18:49 +0100"
include/version.h.bak
View file @ f18dccae
......@@ -12,6 +12,6 @@
#define VERSION "v0.3.0"
#define REVISION "g0690723"
#define TIME "2018-10-02 21:03:46 +0200"
#define REVISION "g664b3dd"
#define TIME "2018-11-11 17:18:49 +0100"
libs/biofiles.c
View file @ f18dccae
......@@ -1586,7 +1586,7 @@ bl_fastxAddMate(void *space,
if(bl_fastaCheckMateID(f, n, descr, descrlen) == 0) {
NFO("The fasta/fastq IDs in both mate files do not match.\n", NULL);
NFO("The first mismatch occured at fastq number %u\n", n);
NFO("The first mismatch occurred at fastq number %u\n", n);
NFO("Exiting.\n", NULL);
exit(EXIT_FAILURE);
}
......@@ -3448,7 +3448,7 @@ bl_annotationRead (void *space, char *fn) {
} else if(!strcmp(suf, ".gff") || !strcmp(suf, ".gff3")) {
annot = bl_GFFread(NULL, fn);
} else {
NFO("please provide a bed or gff file with the approriate extension.\n", NULL);
NFO("please provide a bed or gff file with the appropriate extension.\n", NULL);
exit(EXIT_FAILURE);
}
return annot;
......
libs/gzidx.c
View file @ f18dccae
......@@ -554,7 +554,7 @@ int bl_bgzFillStream(FILE *fp, unsigned char *input, z_stream *strm) {
n = fread(&input[strm->avail_in], 1, CHUNK-strm->avail_in, fp);
if (ferror(fp)) {
fprintf(stderr, "error reading bgz file.\n");
perror("The following error occured:");
perror("The following error occurred:");
exit(EXIT_FAILURE);
}
......
libs/haarz.c
View file @ f18dccae
......@@ -413,7 +413,7 @@ int main(int argc,char** argv) {
prg = manopt_getopts(&prgset, MIN(argc,2), argv);
if(prg->noofvalues == 1) {
manopt_help(&prgset, "programm needs to be selected\n");
manopt_help(&prgset, "program needs to be selected\n");
}
manopt_initoptionset(&optset, argv[0], NULL,
......@@ -833,7 +833,7 @@ int main(int argc,char** argv) {
}
bl_BEDwrite(ptr, mspl.noofitems, stdout);
//bl_BEDwrite(ptr, mspl.noofitems, stdout);
NFO("summarizing %d splits.\n", mspl.noofitems);
bl_splitSummarize(stdout, &mspl, mintotalsplit, minmedianqual, nostrand);
......@@ -848,7 +848,7 @@ int main(int argc,char** argv) {
FREEMEMORY(NULL, unflagged);
} else {
manopt_help(&prgset, "unkown program selected\n");
manopt_help(&prgset, "unknown program selected\n");
}
manopt_destructoptionset(&optset);
......
libs/manopt.c
View file @ f18dccae
......@@ -1039,7 +1039,7 @@ manopt_checkconstraint(manopt_optionset* optset,
case MANOPT_BLOCKSEPARATOR:
break;
default:
manopt_help(optset, "unkown option %s type\n", argset->args[arg].flagname);
manopt_help(optset, "unknown option %s type\n", argset->args[arg].flagname);
break;
}
......
libs/multicharseq.c
View file @ f18dccae
......@@ -423,7 +423,7 @@ initMultiCharSeqAlignment(
a->refstart = MAX(sub_start, (Lint)pos-loff);
if(a->refstart > sub_end) {
fprintf(stderr, "refstart > substart: skiping MultiCharSeqAlignment\n");
fprintf(stderr, "refstart > substart: skipping MultiCharSeqAlignment\n");
return 0;
}
......@@ -480,7 +480,7 @@ initMultiCharSeqAlignmentOpt(
//this should not happen
if(a->refstart > sub_end) {
fprintf(stderr, "refstart > substart: skiping MultiCharSeqAlignment\n");
fprintf(stderr, "refstart > substart: skipping MultiCharSeqAlignment\n");
return 0;
}
......
libs/samio.c
View file @ f18dccae
......@@ -1292,7 +1292,7 @@ bl_samprintSamlist (samlist_t *l, mapping_t* m, segemehl_t *nfo)
bl_samcloseDevice(fx, nfo);
fx = NULL;
}
} else {
} else if(nfo->bamdev) {
for(i=0; i < l->noofrecs; i++) {
bl_bamPrintBamrec(nfo->bamdev, &l->recs[i], nfo->bamhdr, nfo->mtx3);
}
......@@ -1378,10 +1378,14 @@ bl_samprintEmptyAlign (char *desc, char* seq, char* qual, char hasPaired,
bl_samsetMultipleHits(&samlist->recs[0], 1);
bl_samsetMatchId(&samlist->recs[0], 0);
dev = bl_samgetDevice(NULL, &fx, nfo);
bl_samprintSamrec(dev, &samlist->recs[0], lf);
bl_samcloseDevice(fx, nfo);
if(!nfo->bamdev) {
dev = bl_samgetDevice(NULL, &fx, nfo);
bl_samprintSamrec(dev, &samlist->recs[0], lf);
bl_samcloseDevice(fx, nfo);
} else {
bl_bamPrintBamrec(nfo->bamdev, &samlist->recs[0], nfo->bamhdr, nfo->mtx3);
}
bl_samdestructSamList(samlist);
FREEMEMORY(NULL, samlist);
......