From a28e5b0a4f5799e14ed3079e10d481e5b5b4faa9 Mon Sep 17 00:00:00 2001
From: Renato Alves <alves.rjc@gmail.com>
Date: Sat, 17 Oct 2020 12:26:20 +0200
Subject: [PATCH 1/3] samtools: 1.10 -> 1.11

---
 pkgs/applications/science/biology/samtools/default.nix | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pkgs/applications/science/biology/samtools/default.nix b/pkgs/applications/science/biology/samtools/default.nix
index e750eea89ac..27ed79a1f6c 100644
--- a/pkgs/applications/science/biology/samtools/default.nix
+++ b/pkgs/applications/science/biology/samtools/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "samtools";
-  version = "1.10";
+  version = "1.11";
 
   src = fetchurl {
     url = "https://github.com/samtools/samtools/releases/download/${version}/${pname}-${version}.tar.bz2";
-    sha256 = "119ms0dpydw8dkh3zc4yyw9zhdzgv12px4l2kayigv31bpqcb7kv";
+    sha256 = "1dp5wknak4arnw5ghhif9mmljlfnw5bgm91wib7z0j8wdjywx0z2";
   };
 
   nativeBuildInputs = [ perl ];
@@ -29,6 +29,6 @@ stdenv.mkDerivation rec {
     license = licenses.mit;
     homepage = "http://www.htslib.org/";
     platforms = platforms.unix;
-    maintainers = [ maintainers.mimame ];
+    maintainers = with maintainers; [ mimame unode ];
   };
 }

From 6e19ed0a526598087c08bd4ea389394115a6360f Mon Sep 17 00:00:00 2001
From: Renato Alves <alves.rjc@gmail.com>
Date: Thu, 29 Oct 2020 13:27:45 +0100
Subject: [PATCH 2/3] lumpy: 0.3.0 -> 0.3.1

---
 pkgs/applications/science/biology/lumpy/default.nix | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/pkgs/applications/science/biology/lumpy/default.nix b/pkgs/applications/science/biology/lumpy/default.nix
index 04512e8e372..f6267a2e017 100644
--- a/pkgs/applications/science/biology/lumpy/default.nix
+++ b/pkgs/applications/science/biology/lumpy/default.nix
@@ -7,13 +7,14 @@ let
 
 in stdenv.mkDerivation rec {
   pname = "lumpy";
-  version = "0.3.0";
+  version = "0.3.1";
 
   src = fetchFromGitHub {
     owner = "arq5x";
     repo = "lumpy-sv";
-    rev = version;
-    sha256 = "0azhzvmh9az9jcq0xprlzdz6w16azgszv4kshb903bwbnqirmk18";
+    rev = "v${version}";
+    sha256 = "0r71sg7qch8r6p6dw995znrqdj6q49hjdylhzbib2qmv8nvglhs9";
+    fetchSubmodules = true;
   };
 
   nativeBuildInputs = [ which ];
@@ -26,6 +27,8 @@ in stdenv.mkDerivation rec {
     # Use Nix htslib over bundled version
     sed -i 's/lumpy_filter: htslib/lumpy_filter:/' Makefile
     sed -i 's|../../lib/htslib/libhts.a|-lhts|' src/filter/Makefile
+    # Also make sure we use the includes from Nix's htslib
+    sed -i 's|../../lib/htslib/|${htslib}|' src/filter/Makefile
   '';
 
   # Upstream's makefile doesn't have an install target

From 459c5ec3b19767b96ef11225d60b0964c467f3b1 Mon Sep 17 00:00:00 2001
From: Renato Alves <alves.rjc@gmail.com>
Date: Thu, 29 Oct 2020 16:20:23 +0100
Subject: [PATCH 3/3] pythonPackages.pysam: Disable failing tests unrelated to
 packaging

These will be fixed upstream and are due to format changes introduced
in samtools and htslib 1.11
---
 pkgs/development/python-modules/pysam/default.nix | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/pkgs/development/python-modules/pysam/default.nix b/pkgs/development/python-modules/pysam/default.nix
index 2802b6d0e0f..2f40a297333 100644
--- a/pkgs/development/python-modules/pysam/default.nix
+++ b/pkgs/development/python-modules/pysam/default.nix
@@ -80,13 +80,19 @@ buildPythonPackage rec {
       --deselect tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected \
       --deselect tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works \
       --deselect tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected \
-      --deselect tests/AlignmentFile_test.py::TestIO::testBAM2SAM \
-      --deselect tests/AlignmentFile_test.py::TestIO::testSAM2BAM \
-      --deselect tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile \
       --deselect tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile \
       --deselect tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader \
       --deselect tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader \
+      --deselect tests/AlignmentFile_test.py::TestIO::testBAM2BAM \
+      --deselect tests/AlignmentFile_test.py::TestIO::testBAM2CRAM \
+      --deselect tests/AlignmentFile_test.py::TestIO::testBAM2SAM \
+      --deselect tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject \
+      --deselect tests/AlignmentFile_test.py::TestIO::testOpenFromFilename \
+      --deselect tests/AlignmentFile_test.py::TestIO::testSAM2BAM \
+      --deselect tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile \
+      --deselect tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate \
       --deselect tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing \
+      --deselect tests/compile_test.py::BAMTest::testCount \
       tests/
   '';