Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv3004
Modified Files:
vcftools.info vcftools.patch
Log Message:
vcftools 1.1.11
Index: vcftools.info
===================================================================
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/vcftools.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- vcftools.info 30 Jan 2013 21:03:48 -0000 1.1
+++ vcftools.info 16 Aug 2013 02:02:07 -0000 1.2
@@ -1,13 +1,14 @@
Package: vcftools
-Version: 0.1.10
+Version: 0.1.11
Revision: 1
Description: Tools for VCF files
License: GPL
Maintainer: Hanspeter Niederstrasser <nie...@users.sourceforge.net>
Source: mirror:sourceforge:%n/%n_%v.tar.gz
-Source-MD5: c21f0d1be99e98571ef6422da4765f2a
+Source-MD5: ddb49e9fa2bfedae36b4dce163adfaa8
+Source-Checksum: SHA1(00081e99c0f66316d92ee356580885331cadb46f)
PatchFile: %n.patch
-PatchFile-MD5: 7150c38873d6facd46b034a22938a27c
+PatchFile-MD5: 18ee79a2944a86c019711594535e7cc6
#PatchScript: <<
# %{default_script}
#<<
Index: vcftools.patch
===================================================================
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/vcftools.patch,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- vcftools.patch 30 Jan 2013 21:03:49 -0000 1.1
+++ vcftools.patch 16 Aug 2013 02:02:07 -0000 1.2
@@ -1,6 +1,6 @@
-diff -ruN vcftools_0.1.10-orig/Makefile vcftools_0.1.10/Makefile
---- vcftools_0.1.10-orig/Makefile 2012-12-04 03:27:43.000000000 -0500
-+++ vcftools_0.1.10/Makefile 2013-01-14 10:58:09.000000000 -0500
+diff -ruN vcftools_0.1.11-orig/Makefile vcftools_0.1.11/Makefile
+--- vcftools_0.1.11-orig/Makefile 2013-06-13 10:40:56.000000000 -0400
++++ vcftools_0.1.11/Makefile 2013-08-15 21:47:45.000000000 -0400
@@ -17,12 +17,17 @@
export PREFIX = $(dir $(realpath $(lastword $(MAKEFILE_LIST))))
endif
@@ -12,23 +12,23 @@
DIRS = cpp perl
+
+vcftools:
-+ for dir in $(DIRS); do cd $$dir && $(MAKE) && cd ..; done
-+
++ for dir in $(DIRS); do cd $$dir && $(MAKE) && cd ..; done
++
install:
- @mkdir -p $(BINDIR); mkdir -p $(MODDIR); \
- for dir in $(DIRS); do cd $$dir && $(MAKE) $(MAKEFLAGS) && cd ..; done
-+ mkdir -p $(DESTDIR)$(BINDIR); mkdir -p $(DESTDIR)$(MODDIR);
-+ for dir in $(DIRS); do cd $$dir && $(MAKE) install && cd ..; done
++ mkdir -p $(DESTDIR)$(BINDIR); mkdir -p $(DESTDIR)$(MODDIR); \
++ for dir in $(DIRS); do cd $$dir && $(MAKE) install && cd ..; done
clean:
@for dir in $(DIRS); do cd $$dir && $(MAKE) clean && cd ..; done
-diff -ruN vcftools_0.1.10-orig/cpp/Makefile vcftools_0.1.10/cpp/Makefile
---- vcftools_0.1.10-orig/cpp/Makefile 2012-12-04 03:27:39.000000000 -0500
-+++ vcftools_0.1.10/cpp/Makefile 2013-01-14 10:46:35.000000000 -0500
-@@ -36,8 +36,10 @@
+diff -ruN vcftools_0.1.11-orig/cpp/Makefile vcftools_0.1.11/cpp/Makefile
+--- vcftools_0.1.11-orig/cpp/Makefile 2013-06-13 10:40:54.000000000 -0400
++++ vcftools_0.1.11/cpp/Makefile 2013-08-15 21:49:08.000000000 -0400
+@@ -39,8 +39,10 @@
vcftools: $(OBJS)
- $(CPP) $(OBJS) -o vcftools $(LIB)
+ $(CPP) $(CPPFLAGS) $(OBJS) -o vcftools $(LIB)
+
+install:
ifdef BINDIR
@@ -36,16 +36,11 @@
+ cp $(CURDIR)/vcftools $(DESTDIR)$(BINDIR)/vcftools
endif
- # pull in dependency info for *existing* .o files
-diff -ruN vcftools_0.1.10-orig/perl/Makefile vcftools_0.1.10/perl/Makefile
---- vcftools_0.1.10-orig/perl/Makefile 2012-12-04 03:27:41.000000000 -0500
-+++ vcftools_0.1.10/perl/Makefile 2013-01-14 10:45:40.000000000 -0500
-@@ -1,12 +1,14 @@
-
--BIN = fill-aa fill-an-ac fill-fs fill-ref-md5 fill-rsIDs vcf-annotate
vcf-compare vcf-concat \
-- vcf-consensus vcf-contrast vcf-convert vcf-filter vcf-fix-ploidy
vcf-indel-stats vcf-isec vcf-merge vcf-phased-join \
-+BIN = fill-aa fill-an-ac fill-fs fill-ref-md5 vcf-annotate vcf-compare
vcf-concat \
-+ vcf-consensus vcf-contrast vcf-convert vcf-fix-ploidy vcf-indel-stats
vcf-isec vcf-merge vcf-phased-join \
+ bgzf: bgzf.c
+diff -ruN vcftools_0.1.11-orig/perl/Makefile vcftools_0.1.11/perl/Makefile
+--- vcftools_0.1.11-orig/perl/Makefile 2013-06-13 10:40:56.000000000 -0400
++++ vcftools_0.1.11/perl/Makefile 2013-08-15 21:50:26.000000000 -0400
+@@ -4,9 +4,11 @@
vcf-query vcf-shuffle-cols vcf-sort vcf-stats vcf-subset vcf-to-tab
vcf-tstv vcf-validator
MOD = FaSlice.pm Vcf.pm VcfStats.pm
------------------------------------------------------------------------------
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