Codebase list augustus / 3fc379f
refresh patches Sascha Steinbiss 4 years ago
4 changed file(s) with 16 addition(s) and 173 deletion(s). Raw diff Collapse all Expand all
+13
-37
debian/patches/buildflags.patch less more
2424
2525 INCLS = -I../include
2626 LIBS =
27 @@ -36,10 +36,10 @@
28 .SUFFIXES: .cc .o .so
29
30 .cc.o:
31 - $(CC) -c $(CFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $@ $< $(INCLS)
32 + $(CC) -c $(CXXFLAGS) $(CPPFLAGS) -o $@ $< $(INCLS)
33
34 homGeneMapping: main.cc $(OBJS)
35 - $(CC) $(CFLAGS) $(CPPFLAGS) -o $@ $^ $(INCLS) $(LIBS)
36 + $(CC) $(CXXFLAGS) $(CPPFLAGS) -o $@ $^ $(INCLS) $(LDFLAGS) $(LIBS)
37 cp homGeneMapping ../../../bin/homGeneMapping
38
39 clean:
4027 --- a/src/Makefile
4128 +++ b/src/Makefile
42 @@ -68,7 +68,7 @@
43 .SUFFIXES: .cc .o .so
29 @@ -69,7 +69,7 @@
30 .PHONY: googletest
4431
4532 .cc.o:
4633 - $(CXX) -c $(CXXFLAGS) -o $@ $< $(INCLS)
7865 rm -rf *o joingenes; rm -rf ../../bin/joingenes
7966 --- a/auxprogs/bam2hints/Makefile
8067 +++ b/auxprogs/bam2hints/Makefile
81 @@ -12,15 +12,15 @@
82 LIBS = -lbamtools -lz
83 SOURCES = bam2hints.cc
84 OBJECTS = $(SOURCES:.cc=.o)
85 -CXXFLAGS += -Wall -O2 # -g -p -g -ggdb
86 +CXXFLAGS := -Wall -O2 $(CXXFLAGS) # -g -p -g -ggdb
87
88 LINK.cc = g++
89
90 # Recipe(s)
91 -# $@: full target name of current target.
92 -# $<: .c file of target.
93 -bam2hints : $(OBJECTS)
94 - $(LINK.cc) $(CXXFLAGS) $(LDFLAGS) -o $@ $(OBJECTS) $(LIBS)
95 +# $@: full target name of current target.
96 +# $<: .c file of target.
97 +bam2hints : $(OBJECTS)
98 + $(LINK.cc) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(OBJECTS) $(LIBS)
68 @@ -20,7 +20,7 @@
69 # $@: full target name of current target.
70 # $<: .c file of target.
71 bam2hints : $(OBJECTS)
72 - $(LINK.cc) $(CXXFLAGS) $(LDFLAGS) -o $@ $(OBJECTS) $(LIBS)
73 + $(LINK.cc) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $@ $(OBJECTS) $(LIBS)
74 mkdir -p ../../bin
9975 cp bam2hints ../../bin
10076
101 all:$(OBJECTS) # Compiles each foo.cc into foo.o
10277 --- a/auxprogs/bam2wig/Makefile
10378 +++ b/auxprogs/bam2wig/Makefile
104 @@ -21,16 +21,16 @@
105 TABIX=$(TOOLDIR)/tabix/
106 INCLUDES=-I$(SAMTOOLS) -I. -I$(HTSLIB) -I$(BCFTOOLS) -I$(TABIX)
79 @@ -20,17 +20,17 @@
80 BCFTOOLS=$(TOOLDIR)/bcftools
81 INCLUDES=-I$(SAMTOOLS) -I. -I$(HTSLIB) -I$(BCFTOOLS)
10782 VPATH=$(SAMTOOLS)
10883 -LIBS=$(SAMTOOLS)/libbam.a $(HTSLIB)/libhts.a -lcurses -lm -lz -lpthread -lcurl -lssl -lcrypto
10984 -CFLAGS=-Wall -O2 $(INCLUDES)
11590 $(PROGRAM) : bam2wig.o
11691 - $(CC) $(CFLAGS) $^ -o $@ $(LIBS) -lbz2 -llzma
11792 + $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) $^ -o $@ $(LIBS) -lbz2 -llzma
93 mkdir -p ../../bin
11894 cp bam2wig ../../bin/bam2wig
11995
12096 bam2wig.o : bam2wig.c
+3
-3
debian/patches/keep_cflags less more
11 Author: Sascha Steinbiss <sascha@steinbiss.name>
22 --- a/src/Makefile
33 +++ b/src/Makefile
4 @@ -118,7 +118,7 @@
4 @@ -119,7 +119,7 @@
55 echo "$(CXXFLAGS)" > $(INFO)
66
77 clean:
88 - rm -f ../bin/* $(PROGR) $(OBJS) $(DUMOBJS) $(TOBJS) consensus.o exon_seg.o pp_fastBlockSearcher.o $(INFO)
99 + rm -f ../bin/* $(PROGR) $(OBJS) $(DUMOBJS) $(TOBJS) consensus.o exon_seg.o pp_fastBlockSearcher.o
10 cd googletest && ${MAKE} clean
11 cd unittests && ${MAKE} clean
1012
11 tidy: clean
12 rm -f *~ *.o *.rej *.orig ../include/*~ ../include/*.orig ../include/*.rej $(INFO)
+0
-1
debian/patches/series less more
22 keep_cflags
33 buildflags.patch
44 interpreter_paths.patch
5 spelling.patch
+0
-132
debian/patches/spelling.patch less more
0 Description: spelling patches
1 Author: Sascha Steinbiss <satta@debian.org>
2 --- a/auxprogs/bam2hints/bam2hints.cc
3 +++ b/auxprogs/bam2hints/bam2hints.cc
4 @@ -541,7 +541,7 @@
5 << " CACW21662.g1 3 C2 5TNS Unknown\n"
6 << " CACW25491.g1 3 F21 5TNS 3TNS-NP\n"
7 */
8 - << " --maxgenelen=n -G alignments of the same clone are considered to be of the same gene if not separeted by more than this (set to " << MaxGeneLen << ")\n"
9 + << " --maxgenelen=n -G alignments of the same clone are considered to be of the same gene if not separated by more than this (set to " << MaxGeneLen << ")\n"
10 << " Alignments that span more than this are ignored, but better filter long introns through an alignment program.\n"
11 << " --help -h show this help text\n"
12 << "\n";
13 --- a/auxprogs/homGeneMapping/README.TXT
14 +++ b/auxprogs/homGeneMapping/README.TXT
15 @@ -66,7 +66,7 @@
16 --halLiftover_exec_dir=DIR Directory that contains the executable halLiftover from the HAL Tools package
17 If not specified it must be in $PATH environment variable.
18 --tmpdir=DIR a temporary file directory that stores lifted over files. (default 'tmp/' in current directory)
19 ---outdir=DIR file direcory that stores output gene files. (default: current directory)
20 +--outdir=DIR file directory that stores output gene files. (default: current directory)
21
22 example:
23 homGeneMapping --noDupes --halLiftOver_exec_dir=~/tools/progressiveCactus/submodules/hal/bin --gtfs=gtffilenames.tbl --halfile=msca.hal
24 --- a/auxprogs/homGeneMapping/src/main.cc
25 +++ b/auxprogs/homGeneMapping/src/main.cc
26 @@ -293,7 +293,7 @@
27 --unmapped print a GTF attribute with a list of all genomes, that are not aligned to the\n\
28 corresponding gene feature, e.g. hgm_unmapped \"1,4,5\"; (default; off)\n\
29 --tmpdir=DIR a temporary file directory that stores lifted over files. (default 'tmp/' in current directory)\n\
30 ---outdir=DIR file direcory that stores output gene files. (default: current directory)\n\
31 +--outdir=DIR file directory that stores output gene files. (default: current directory)\n\
32 --printHomologs=FILE prints disjunct sets of homologous transcripts to FILE, e.g.\n\
33 # 0 dana\n\
34 # 1 dere\n\
35 --- a/mansrc/bam2hints.1
36 +++ b/mansrc/bam2hints.1
37 @@ -110,7 +110,7 @@
38 .sp
39 \fB\-\-maxgenelen=n\fP/\fB\-G\fP
40 .RS 4
41 -alignments of the same clone are considered to be of the same gene if not separeted by more than this (set to 400000). Alignments that span more than this are ignored, but better filter long introns through an alignment program.
42 +alignments of the same clone are considered to be of the same gene if not separated by more than this (set to 400000). Alignments that span more than this are ignored, but better filter long introns through an alignment program.
43 .RE
44 .SH "AUTHORS"
45 .sp
46 --- a/mansrc/bam2hints.1.adoc
47 +++ b/mansrc/bam2hints.1.adoc
48 @@ -63,7 +63,7 @@
49 fill this number in in the score column (set to 0)
50
51 *--maxgenelen=n*/*-G*::
52 - alignments of the same clone are considered to be of the same gene if not separeted by more than this (set to 400000). Alignments that span more than this are ignored, but better filter long introns through an alignment program.
53 + alignments of the same clone are considered to be of the same gene if not separated by more than this (set to 400000). Alignments that span more than this are ignored, but better filter long introns through an alignment program.
54
55 ## AUTHORS
56
57 --- a/mansrc/homGeneMapping.1
58 +++ b/mansrc/homGeneMapping.1
59 @@ -112,7 +112,7 @@
60 .sp
61 \fB\-\-outdir=DIR\fP
62 .RS 4
63 -file direcory that stores output gene files. (default: current directory)
64 +file directory that stores output gene files. (default: current directory)
65 .RE
66 .sp
67 \fB\-\-printHomologs=FILE\fP
68 --- a/mansrc/homGeneMapping.1.adoc
69 +++ b/mansrc/homGeneMapping.1.adoc
70 @@ -50,7 +50,7 @@
71 a temporary file directory that stores lifted over files. (default 'tmp/' in current directory)
72
73 *--outdir=DIR*::
74 - file direcory that stores output gene files. (default: current directory)
75 + file directory that stores output gene files. (default: current directory)
76
77 *--printHomologs=FILE*::
78 prints disjunct sets of homologous transcripts to FILE, e.g.
79 --- a/scripts/autoAugPred.pl
80 +++ b/scripts/autoAugPred.pl
81 @@ -470,7 +470,7 @@
82 chdir "$workDir" or die ("Error: Could not change directory to $workDir. Please specify a valid one!\n");
83 }
84 else{
85 - die("Error: Missing working direcory!\n$usage");
86 + die("Error: Missing working directory!\n$usage");
87 }
88
89 if(-f "your_job.tmp"){
90 --- a/scripts/blat2hints.pl
91 +++ b/scripts/blat2hints.pl
92 @@ -52,7 +52,7 @@
93 $usage .= " CACW25491.g1 3 F21 5TNS 3TNS-NP\n";
94 $usage .= " \n";
95 $usage .= " cloneB\tread4\tread5\n";
96 -$usage .= " --maxgenelen=n alignments of the same clone are considered to be of the same gene if not separeted by more than this (400000)\n";
97 +$usage .= " --maxgenelen=n alignments of the same clone are considered to be of the same gene if not separated by more than this (400000)\n";
98 $usage .= " Alignments that span more than this are ignored, but better filter long introns through alignment program.\n";
99
100 my $blatfilename;
101 --- a/src/motif.cc
102 +++ b/src/motif.cc
103 @@ -193,7 +193,7 @@
104 // cout <<"Gewichtungsmatrix: \n" << weighingMatrix << endl;
105 istrm.close();
106 } else {
107 - string errorMess("Could't open the file with the weight matrix: ");
108 + string errorMess("Couldn't open the file with the weight matrix: ");
109 errorMess.append(matrixFileName);
110 throw ProjectError(errorMess.c_str());
111 }
112 --- a/src/namgene.cc
113 +++ b/src/namgene.cc
114 @@ -1399,7 +1399,7 @@
115
116 istrm.close();
117 } else {
118 - throw NAMGeneError( "Could't open the file with transition probabilities." );
119 + throw NAMGeneError( "Couldn't open the file with transition probabilities." );
120 }
121 }
122
123 @@ -1449,7 +1449,7 @@
124 istrm >> Constant::tail2tail_ovlp[i];
125 istrm.close();
126 } else {
127 - throw NAMGeneError( "Could't open the file with the overlap length distribution." );
128 + throw NAMGeneError( "Couldn't open the file with the overlap length distribution." );
129 }
130 }
131