[med-svn] [spades] 03/06: new upstream version

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository spades.

commit 109110e372b990796368d61d2328d015cd8e18fc
Author: Sascha Steinbiss <satta at debian.org>
Date:   Sun Jul 24 10:05:16 2016 +0000

    new upstream version
---
 debian/changelog                                   | 7 +++++++
 debian/copyright                                   | 4 ++++
 debian/patches/0003_accept-system-bwa.patch        | 2 +-
 debian/patches/0103_use-debian-packaged-bwa.patch  | 4 ++--
 debian/patches/0111_use_full_config_dirs.patch     | 4 ++--
 debian/patches/0114_use_debian_provided_libs.patch | 2 +-
 debian/patches/0116_stable_link_order.patch        | 2 +-
 7 files changed, 18 insertions(+), 7 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 7dc517b..71aba26 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+spades (3.9.0+dfsg-1) UNRELEASED; urgency=medium
+
+  * New upstream release.
+  * Add copyright entry for cxxopts.
+
+ -- Sascha Steinbiss <satta at debian.org>  Sun, 24 Jul 2016 09:51:30 +0000
+
 spades (3.8.2+dfsg2-1) unstable; urgency=medium
 
   * Make sure bundled headers are not used by cleaning orig tarball.
diff --git a/debian/copyright b/debian/copyright
index 72bc13b..7225ba8 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -303,6 +303,10 @@ Files: ext/include/htrie/*
 Copyright: (c) 2011 Daniel C. Jones <dcjones at cs.washington.edu>
 License: MIT
 
+Files: ext/include/cxxopts/*
+Copyright: (c) 2014, 2015, 2016 Jarryd Beck
+License: MIT
+
 License: MIT
  Permission is hereby granted, free of charge, to any person obtaining a copy
  of this software and associated documentation files (the "Software"), to deal
diff --git a/debian/patches/0003_accept-system-bwa.patch b/debian/patches/0003_accept-system-bwa.patch
index 3ba7cc6..f89d04a 100644
--- a/debian/patches/0003_accept-system-bwa.patch
+++ b/debian/patches/0003_accept-system-bwa.patch
@@ -80,7 +80,7 @@ Description: Enable using Debian packaged bwa instead of bwa-spades
  
  def fill_cfg(options_to_parse, log, secondary_filling=False):
      skip_output_dir=secondary_filling
-@@ -443,7 +459,11 @@
+@@ -456,7 +472,11 @@
      if (not options_storage.only_error_correction) and options_storage.mismatch_corrector:
          cfg["mismatch_corrector"] = empty_config()
          cfg["mismatch_corrector"].__dict__["skip-masked"] = None
diff --git a/debian/patches/0103_use-debian-packaged-bwa.patch b/debian/patches/0103_use-debian-packaged-bwa.patch
index 91a0168..9355359 100644
--- a/debian/patches/0103_use-debian-packaged-bwa.patch
+++ b/debian/patches/0103_use-debian-packaged-bwa.patch
@@ -13,8 +13,8 @@ Description: SPAdes originally contained a code copy of bwa since the version
     ln -s /usr/bin/bwa /usr/lib/spades/bin/bwa-spades
  which enables successfull run of the test suite
 
---- spades.orig/ext/tools/CMakeLists.txt
-+++ spades/ext/tools/CMakeLists.txt
+--- a/ext/tools/CMakeLists.txt
++++ b/ext/tools/CMakeLists.txt
 @@ -5,4 +5,3 @@
  # See file LICENSE for details.
  ############################################################################
diff --git a/debian/patches/0111_use_full_config_dirs.patch b/debian/patches/0111_use_full_config_dirs.patch
index 0807c62..50861da 100644
--- a/debian/patches/0111_use_full_config_dirs.patch
+++ b/debian/patches/0111_use_full_config_dirs.patch
@@ -4,7 +4,7 @@ Description: use full config include path
 Author: Sascha Steinbiss <satta at debian.org>
 --- a/src/spades_pipeline/spades_logic.py
 +++ b/src/spades_pipeline/spades_logic.py
-@@ -179,6 +179,20 @@
+@@ -180,6 +180,20 @@
  
      add_configs(command, dst_configs)
  
@@ -25,7 +25,7 @@ Author: Sascha Steinbiss <satta at debian.org>
      #print("Calling: " + " ".join(command))
      support.sys_call(command, log)
  
-@@ -226,6 +240,19 @@
+@@ -227,6 +241,19 @@
      command = [os.path.join(execution_home, "scaffold_correction"), cfg_file_name]
      add_configs(command, dst_configs)
      log.info(str(command))
diff --git a/debian/patches/0114_use_debian_provided_libs.patch b/debian/patches/0114_use_debian_provided_libs.patch
index 812a66b..e66a3f8 100644
--- a/debian/patches/0114_use_debian_provided_libs.patch
+++ b/debian/patches/0114_use_debian_provided_libs.patch
@@ -89,7 +89,7 @@ Author: Sascha Steinbiss <satta at debian.org>
 @@ -9,4 +9,4 @@
  
  add_library(graph_support STATIC
-             components/connected_component.cpp paths/bidirectional_path.cpp graph_support/scaff_supplementary.cpp)
+             components/connected_component.cpp paths/bidirectional_path.cpp graph_support/scaff_supplementary.cpp graph_alignment/edge_index_refiller.cpp)
 -target_link_libraries(graph_support hattrie)
 +target_link_libraries(graph_support hat-trie)
 --- a/src/modules/assembly_graph/graph_alignment/kmer_map.hpp
diff --git a/debian/patches/0116_stable_link_order.patch b/debian/patches/0116_stable_link_order.patch
index f1e972f..73e4288 100644
--- a/debian/patches/0116_stable_link_order.patch
+++ b/debian/patches/0116_stable_link_order.patch
@@ -2,7 +2,7 @@ Description: use stable sort order for file globbing
 Author: Sascha Steinbiss <satta at debian.org>
 --- a/ext/src/llvm/CMakeLists.txt
 +++ b/ext/src/llvm/CMakeLists.txt
-@@ -29,6 +29,7 @@
+@@ -26,6 +26,7 @@
                 ${SPADES_BUILT_INCLUDE_DIR}/llvm/Config.h)
  
  file(GLOB sources "[a-zA-Z]*.cpp" "[a-zA-Z]*.c")

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