bamutil builds with newer gcc's (#10229)

The most recent release of bamutil that we support uses an embedded
copy of libStatGen that has several issues that keep it from building
with newer releases of gcc.

They've all been fixed upstream and the latest release of bamutil
would pick them up if/when we support it.  The build process has
changed though, plus my team needs *this* version.

This commit backports those fixes.

1 files changed, 29 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/bamutil/libstatgen-issue-19.patch b/var/spack/repos/builtin/packages/bamutil/libstatgen-issue-19.patch
new file mode 100644
index 0000000000..86beb5c34e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bamutil/libstatgen-issue-19.patch
@@ -0,0 +1,29 @@
+From 3a10afe08c209dbacc3eca7794a5a8c0a42ee566 Mon Sep 17 00:00:00 2001
+From: jonathonl <jonathonl@users.noreply.github.com>
+Date: Thu, 20 Sep 2018 11:57:06 -0400
+Subject: [PATCH] Removes erroneous deletes in Chromosome constructor.
+
+---
+ general/Chromosome.cpp | 2 --
+ 1 file changed, 2 deletions(-)
+
+diff --git a/general/Chromosome.cpp b/general/Chromosome.cpp
+index ac2ff5c..2d773e8 100644
+--- a/libStatGen/general/Chromosome.cpp
++++ b/libStatGen/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);