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authorToyohisa Kameyama <kameyama@riken.jp>2019-10-04 12:19:58 +0900
committerAdam J. Stewart <ajstewart426@gmail.com>2019-10-03 22:19:58 -0500
commitb89fa3e01a67308ec41398e2a888526b014664cb (patch)
tree0b5d23f624af77f055bb4a81fe7efa7986f689bf
parent4046e10b951cf6c5f420fa125d6bea23103b60f8 (diff)
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fastqvalidator: add zlib dependency and Removes erroneous deletes in Chromosome (#13030)
-rw-r--r--var/spack/repos/builtin/packages/fastqvalidator/chromosome.patch26
-rw-r--r--var/spack/repos/builtin/packages/fastqvalidator/package.py3
2 files changed, 29 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/fastqvalidator/chromosome.patch b/var/spack/repos/builtin/packages/fastqvalidator/chromosome.patch
new file mode 100644
index 0000000000..579444868e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fastqvalidator/chromosome.patch
@@ -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);
diff --git a/var/spack/repos/builtin/packages/fastqvalidator/package.py b/var/spack/repos/builtin/packages/fastqvalidator/package.py
index 4395892e17..9397eec2a0 100644
--- a/var/spack/repos/builtin/packages/fastqvalidator/package.py
+++ b/var/spack/repos/builtin/packages/fastqvalidator/package.py
@@ -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(