gentoo-overlay/sci-biology/pysam/files/pysam-0.9.0-missing-config.h.patch

From 55f5d8ce51ad999123a779f31fcf0fecd60de9e6 Mon Sep 17 00:00:00 2001
From: Andreas Heger <andreas.heger@gmail.com>
Date: Mon, 21 Mar 2016 21:10:04 +0000
Subject: [PATCH] {AH} create empty config.h for samtools if it does not exist,
 fixes #245

---
 setup.py | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 7b59b69..2f00c37 100644
--- a/setup.py
+++ b/setup.py
@@ -155,7 +155,7 @@ def run_configure(option):
             outf.write(
                 "/* empty config.h created by pysam */\n")
             outf.write(
-                "/* conservative compilation options */")
+                "/* conservative compilation options */\n")
 
 if HTSLIB_LIBRARY_DIR:
     # linking against a shared, externally installed htslib version, no
@@ -259,6 +259,16 @@ def run_configure(option):
                "adding shared libcurl and libcrypto")
         external_htslib_libraries.extend(["curl", "crypto"])
 
+# create empty config.h files if they have not been created automatically
+# or created by the user:
+for fn in "samtools/config.h", "htslib/config.h":
+    if not os.path.exists(fn):
+        with open(fn, "w") as outf:
+            outf.write(
+                "/* empty config.h created by pysam */\n")
+            outf.write(
+                "/* conservative compilation options */\n")
+
 parts = ["samtools",
          "bcftools",
          "htslib",