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Removed unused var2vcf subprogram
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jts committed Mar 12, 2013
1 parent aed4754 commit 6bb3efb
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Showing 4 changed files with 0 additions and 490 deletions.
1 change: 0 additions & 1 deletion src/SGA/Makefile.am
Expand Up @@ -49,7 +49,6 @@ sga_SOURCES = sga.cpp \
gen-ssa.h gen-ssa.cpp \
bwt2fa.h bwt2fa.cpp \
graph-diff.h graph-diff.cpp \
var2vcf.h var2vcf.cpp \
hapgen.h hapgen.cpp \
gapfill.h gapfill.cpp \
variant-detectability.h variant-detectability.cpp \
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4 changes: 0 additions & 4 deletions src/SGA/sga.cpp
Expand Up @@ -31,7 +31,6 @@
#include "bwt2fa.h"
#include "graph-diff.h"
#include "hapgen.h"
#include "var2vcf.h"
#include "gapfill.h"
#include "variant-detectability.h"
#include "rewrite-evidence-bam.h"
Expand Down Expand Up @@ -77,7 +76,6 @@ static const char *SGA_USAGE_MESSAGE =
" filterBAM filter out contaminating mate-pair data in a BAM file\n"
" cluster find clusters of reads belonging to the same connected component in an assembly graph\n"
//" connect resolve the complete sequence of a paired-end fragment\n"
//" var2vcf convert aligned variant sequences found by graph-diff into a VCF file\n"
//" hapgen generate candidate haplotypes from an assembly graph\n"
"\nReport bugs to " PACKAGE_BUGREPORT "\n\n";

Expand Down Expand Up @@ -146,8 +144,6 @@ int main(int argc, char** argv)
bwt2faMain(argc - 1, argv + 1);
else if(command == "graph-diff")
graphDiffMain(argc - 1, argv + 1);
else if(command == "var2vcf")
var2vcfMain(argc - 1, argv + 1);
else if(command == "hapgen")
hapgenMain(argc - 1, argv + 1);
else if(command == "gapfill")
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