From 070325de8dc48e196f3503d5b213c4d8bed47ca3 Mon Sep 17 00:00:00 2001
From: Afif Elghraoui <afif@debian.org>
Date: Sun, 10 Sep 2017 00:15:40 -0400
Subject: [PATCH] New upstream version 0.12.0.1+ds

---
 MANIFEST.in         | 8 ++++++++
 bcftools/config.h   | 2 ++
 doc/release.rst     | 7 +++++++
 pysam/version.py    | 2 +-
 run_tests_travis.sh | 2 ++
 setup.py            | 7 ++++++-
 6 files changed, 26 insertions(+), 2 deletions(-)
 create mode 100644 bcftools/config.h

diff --git a/MANIFEST.in b/MANIFEST.in
index 3f2a9cb..20b7777 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -15,12 +15,20 @@ include pysam/libc*.pyx
 include pysam/libc*.c
 include pysam/*.c
 include pysam/*.h
+
+# samtools
 include samtools/configure
 include samtools/config.mk.in
 include samtools/config.h.in
 include samtools/*.h
 exclude samtools/config.h
 include samtools/*/*.h
+
+# bcftools
+include bcftools/*.h
+exclude bcftools/config.h
+
+# htslib
 include htslib/*.c
 include htslib/*.h
 exclude htslib/config.h
diff --git a/bcftools/config.h b/bcftools/config.h
new file mode 100644
index 0000000..f8fff59
--- /dev/null
+++ b/bcftools/config.h
@@ -0,0 +1,2 @@
+/* empty config.h created by pysam */
+/* conservative compilation options */
diff --git a/doc/release.rst b/doc/release.rst
index 4a9b35c..18af4ad 100644
--- a/doc/release.rst
+++ b/doc/release.rst
@@ -2,6 +2,12 @@
 Release notes
 =============
 
+Release 0.12.0.1
+================
+
+Bugfix release to solve compilation issue due to missinge
+bcftools/config.h file.
+
 Release 0.12.0
 ==============
 
@@ -31,6 +37,7 @@ contains a series of bugfixes.
 * [#496] upgrade to htslib/samtools/bcftools versions 1.5
 * add start/stop to AlignmentFile.fetch() to be consistent with
   VariantFile.fetch(). "end" is kept for backwards compatibility.
+* [#512] add get_index_statistics() method to AlignmentFile.
 
 Upcoming changes:
 
diff --git a/pysam/version.py b/pysam/version.py
index 89cf2de..2a416f1 100644
--- a/pysam/version.py
+++ b/pysam/version.py
@@ -1,5 +1,5 @@
 # pysam versioning information
-__version__ = "0.12"
+__version__ = "0.12.0.1"
 
 # TODO: upgrade number
 __samtools_version__ = "1.5"
diff --git a/run_tests_travis.sh b/run_tests_travis.sh
index 45c928e..fa44857 100755
--- a/run_tests_travis.sh
+++ b/run_tests_travis.sh
@@ -85,6 +85,8 @@ echo "checking for presence of config.h files in tar-ball"
 tar -tvzf dist/pysam-*.tar.gz | grep "config.h$"
 
 if [ $? != 1 ]; then
+    echo "ERROR: found config.h in tar-ball"
+    tar -tvzf dist/pysam-*.tar.gz | grep "config.h%"
     exit 1
 fi
 
diff --git a/setup.py b/setup.py
index 5b23d20..66783ae 100644
--- a/setup.py
+++ b/setup.py
@@ -134,7 +134,12 @@ package_list = ['pysam',
 package_dirs = {'pysam': 'pysam',
                 'pysam.include.samtools': 'samtools',
                 'pysam.include.bcftools': 'bcftools'}
-config_headers = ["samtools/config.h"]
+
+# list of config files that will be automatically generated should
+# they not already exist or be created by configure scripts in the
+# subpackages.
+config_headers = ["samtools/config.h",
+                  "bcftools/config.h"]
 
 from cy_build import CyExtension as Extension, cy_build_ext as build_ext
 
-- 
2.30.2