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fastqvalidator: add zlib dependency and Removes erroneous deletes in Chromosome (#13030)

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This commit is contained in:
Toyohisa Kameyama
2019-10-04 12:19:58 +09:00
committed by Adam J. Stewart
parent 4046e10b95
commit b89fa3e01a
2 changed files with 29 additions and 0 deletions
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26
var/spack/repos/builtin/packages/fastqvalidator/chromosome.patch Normal file
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@@ -0,0 +1,26 @@
commit 3a10afe08c209dbacc3eca7794a5a8c0a42ee566
Author: jonathonl <jonathonl@users.noreply.github.com>
Date: Thu Sep 20 11:57:06 2018 -0400
Removes erroneous deletes in Chromosome constructor.
diff --git a/general/Chromosome.cpp b/general/Chromosome.cpp
index ac2ff5c..2d773e8 100644
--- a/general/Chromosome.cpp
+++ b/general/Chromosome.cpp
@@ -27,7 +27,6 @@ Chromosome::Chromosome(GenomeSequence* gs, const char* chromosomeName)
Chromosome::Chromosome(const char* genomseSequenceFileName, unsigned int chromosomeIndex, bool isColorSpace)
{
std::string s(genomseSequenceFileName);
- if (this->gs) delete gs;
gs = new GenomeSequence;
assert(gs);
gs->setReferenceName(s);
@@ -39,7 +38,6 @@ Chromosome::Chromosome(const char* genomseSequenceFileName, unsigned int chromos
Chromosome::Chromosome(const std::string& genomseSequenceFileName, unsigned int chromosomeIndex, bool isColorSpace)
{
- if (this->gs) delete gs;
gs = new GenomeSequence;
assert(gs);
gs->setReferenceName(genomseSequenceFileName);

3
var/spack/repos/builtin/packages/fastqvalidator/package.py
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@@ -20,6 +20,9 @@ class Fastqvalidator(MakefilePackage):
commit='9db9c23e176a6ce6f421a3c21ccadedca892ac0c'
)
depends_on('zlib', type='link')
patch('chromosome.patch', when='@2017-01-10', working_dir='libStatGen')
@property
def build_targets(self):
return ['LIB_PATH_GENERAL={0}'.format(