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denovogear: Add missing zlib depenbdency and fix open handling error. (#13017)

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Toyohisa Kameyama 2019-10-03 02:54:50 +09:00 committed by Adam J. Stewart
parent 58c01792ef
commit b85ff04681
2 changed files with 15 additions and 0 deletions
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3
var/spack/repos/builtin/packages/denovogear/package.py
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@ -22,3 +22,6 @@ class Denovogear(CMakePackage):
depends_on('boost@1.47:1.60', type=('build')) depends_on('boost@1.47:1.60', type=('build'))
depends_on('htslib@1.2:', type=('build')) depends_on('htslib@1.2:', type=('build'))
depends_on('eigen', type=('build')) depends_on('eigen', type=('build'))
depends_on('zlib', type=('link'))
patch('stream-open.patch', when='@:1.1.1')

12
var/spack/repos/builtin/packages/denovogear/stream-open.patch Normal file
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@ -0,0 +1,12 @@
diff -ru spack-src.org/src/dng-dnm.cc spack-src/src/dng-dnm.cc
--- spack-src.org/src/dng-dnm.cc 2015-04-21 09:16:59.000000000 +0900
+++ spack-src/src/dng-dnm.cc 2019-10-02 15:08:28.892042247 +0900
@@ -161,7 +161,7 @@
int writeVCFHeader(std::ofstream& fo_vcf, string op_vcf_f, string bcf_file, string ped_file, string sample)
{
fo_vcf.open(op_vcf_f.c_str());
- if(fo_vcf == NULL) {
+ if(fo_vcf.fail()) {
cerr<<"Unable to open vcf file for writing output. Exiting !"<<endl;
}
fo_vcf<<"##fileformat=VCFv4.1\n";