Commit 2ed0b22f authored by Andreas Tille's avatar Andreas Tille
Browse files

Remove unused old patches, fix linking of zlib

parent 0bfca667

Makefile

+1 −1
Original line number Diff line number Diff line
@@ -42,5 +42,5 @@ check: $(BIN) 


clean:

	rm -vf $(OBJ)

	rm -vf $(BIN)

	rm -v $(BIN)

        # find -name '*.o' -exec rm \{\} \;

debian/patches/001_fix_unit_tests.patch

deleted100644 → 0
+0 −21
Original line number Diff line number Diff line 
Origin: https://github.com/biod/BioD/pull/38/commits/643b454f04f36d66c34304b7186a3d2c24fdf783

From: Matthias Klumpp <matthias@tenstral.net>

Date: Thu, 4 Oct 2018 14:33:37 +0200

Subject: [PATCH] trivial: Fix unittests



---

 test/unittests.d | 1 +

 1 file changed, 1 insertion(+)



diff --git a/test/unittests.d b/test/unittests.d

index d52fb687..263662af 100644

--- a/test/unittests.d

+++ b/test/unittests.d

@@ -22,6 +22,7 @@

 

 */

 

+import bio.bam.cigar;

 import bio.bam.reader;

 import bio.bam.writer;

 import bio.sam.reader;

debian/patches/002_include_bio2.patch

deleted100644 → 0
+0 −66
Original line number Diff line number Diff line 
Origin: https://github.com/biod/BioD/pull/38/commits/ee9428fea0d240ad6a65892346ddc051e086af16

From: Matthias Klumpp <matthias@tenstral.net>

Date: Thu, 4 Oct 2018 14:35:02 +0200

Subject: [PATCH] meson: Include bio2 in libbiod build



---

 meson.build | 21 +++++++++++++++++++--

 1 file changed, 19 insertions(+), 2 deletions(-)



diff --git a/meson.build b/meson.build

index 76da2a00..88f3bcc7 100644

--- a/meson.build

+++ b/meson.build

@@ -89,19 +89,33 @@ biod_src = [

     'bio/sam/utils/recordparser.d',

     'bio/sam/reader.d',

     'bio/sam/header.d'

+

+bio2_src = [

+    'bio2/bam/header.d',

+    'bio2/bam/reader.d',

+    'bio2/bam/writer.d',

+    'bio2/bgzf.d',

+    'bio2/bgzf_writer.d',

+    'bio2/constants.d',

+    'bio2/hashing.d',

+    'bio2/logger.d',

+    'bio2/pileup.d',

+    'bio2/reads.d',

+    'bio2/unpack.d'

 ]

 

 #

 # Includes

 #

-install_subdir('bio/', install_dir: 'include/d/')

+install_subdir('bio/', install_dir: 'include/d/bio/')

+install_subdir('bio2/', install_dir: 'include/d/bio/')

 

 #

 # Library and pkg-config

 #

 biod_lib = library('biod',

-        [biod_src],

         include_directories: [src_dir],

+        [biod_src, bio2_src],

         dependencies: [undead_dep, zlib_dep],

         install: true,

         version: project_version,

@@ -111,6 +125,7 @@ pkgc.generate(name: 'biod',

               libraries: biod_lib,

               subdirs: 'd/',

               version: project_version,

+              subdirs: 'd/bio/',

               description: 'Bioinformatics library in D (utils for working with SAM, BAM, SFF formats).'

 )

 

@@ -121,6 +136,8 @@ biod_test_exe = executable('biod_test',

     ['test/unittests.d',

     biod_src],

     include_directories: [src_dir],

+     biod_src,

+     bio2_src],

     dependencies: [undead_dep, zlib_dep],

     d_args: meson.get_compiler('d').unittest_args()

 )

debian/patches/003_modernize_meson.patch

deleted100644 → 0
+0 −197
Original line number Diff line number Diff line 
From c059165f359327c5a67aadabe18d6016efb58780 Mon Sep 17 00:00:00 2001

From: Matthias Klumpp <matthias@tenstral.net>

Date: Thu, 4 Oct 2018 14:35:24 +0200

Subject: [PATCH] meson: Modernize Meson build definition

Origin: https://github.com/biod/BioD/pull/38/commits/c059165f359327c5a67aadabe18d6016efb58780



---

 meson.build | 131 +++++++++++++++++++++++++++-------------------------

 1 file changed, 67 insertions(+), 64 deletions(-)



--- libbiod.orig/meson.build

+++ libbiod/meson.build

@@ -1,6 +1,9 @@

-project('BioD', 'd')

+project('BioD', 'd',

+    meson_version : '>=0.46',

+    license : 'MIT',

+    version : '0.2.2'

+)

 

-project_version   = '0.1.0'

 project_soversion = '0'

 

 src_dir = include_directories('.')

@@ -16,79 +19,83 @@

 # Sources

 #

 biod_src = [

-    'bio/bam/utils/value.d',

-    'bio/bam/utils/samheadermerger.d',

-    'bio/bam/utils/array.d',

-    'bio/bam/utils/graph.d',

-    'bio/bam/pileup.d',

-    'bio/bam/readrange.d',

-    'bio/bam/reader.d',

-    'bio/bam/thirdparty/msgpack.d',

+    'bio/bam/abstractreader.d',

+    'bio/bam/bai/bin.d',

     'bio/bam/baifile.d',

+    'bio/bam/bai/indexing.d',

+    'bio/bam/baseinfo.d',

+    'bio/bam/cigar.d',

+    'bio/bam/constants.d',

     'bio/bam/iontorrent/flowcall.d',

     'bio/bam/iontorrent/flowindex.d',

-    'bio/bam/splitter.d',

-    'bio/bam/abstractreader.d',

-    'bio/bam/bai/indexing.d',

-    'bio/bam/bai/bin.d',

-    'bio/bam/multireader.d',

-    'bio/bam/reference.d',

-    'bio/bam/md/operation.d',

     'bio/bam/md/core.d',

+    'bio/bam/md/operation.d',

     'bio/bam/md/parse.d',

     'bio/bam/md/reconstruct.d',

-    'bio/bam/tagvalue.d',

-    'bio/bam/validation/alignment.d',

-    'bio/bam/validation/samheader.d',

-    'bio/bam/region.d',

+    'bio/bam/multireader.d',

+    'bio/bam/pileup.d',

     'bio/bam/randomaccessmanager.d',

+    'bio/bam/read.d',

+    'bio/bam/reader.d',

+    'bio/bam/readrange.d',

+    'bio/bam/reference.d',

     'bio/bam/referenceinfo.d',

-    'bio/bam/constants.d',

+    'bio/bam/region.d',

     'bio/bam/snpcallers/maq.d',

     'bio/bam/snpcallers/simple.d',

-    'bio/bam/read.d',

+    'bio/bam/splitter.d',

+    'bio/bam/tagvalue.d',

+    'bio/bam/thirdparty/msgpack.d',

+    'bio/bam/utils/array.d',

+    'bio/bam/utils/graph.d',

+    'bio/bam/utils/samheadermerger.d',

+    'bio/bam/utils/value.d',

+    'bio/bam/validation/alignment.d',

+    'bio/bam/validation/samheader.d',

     'bio/bam/writer.d',

-    'bio/bam/baseinfo.d',

-    'bio/maf/reader.d',

-    'bio/maf/parser.d',

-    'bio/maf/block.d',

-    'bio/core/utils/memoize.d',

-    'bio/core/utils/algo.d',

-    'bio/core/utils/stream.d',

-    'bio/core/utils/zlib.d',

-    'bio/core/utils/tmpfile.d',

-    'bio/core/utils/roundbuf.d',

-    'bio/core/utils/format.d',

-    'bio/core/utils/bylinefast.d',

-    'bio/core/utils/range.d',

-    'bio/core/utils/switchendianness.d',

-    'bio/core/utils/outbuffer.d',

-    'bio/core/genotype.d',

-    'bio/core/fasta.d',

     'bio/core/base.d',

-    'bio/core/kmer.d',

-    'bio/core/region.d',

-    'bio/core/tinymap.d',

-    'bio/core/sequence.d',

-    'bio/core/bgzf/outputstream.d',

+    'bio/core/bgzf/block.d',

     'bio/core/bgzf/chunk.d',

-    'bio/core/bgzf/inputstream.d',

+    'bio/core/bgzf/compress.d',

     'bio/core/bgzf/constants.d',

-    'bio/core/bgzf/block.d',

+    'bio/core/bgzf/inputstream.d',

+    'bio/core/bgzf/outputstream.d',

     'bio/core/bgzf/virtualoffset.d',

-    'bio/core/bgzf/compress.d',

     'bio/core/call.d',

-    'bio/sff/utils/roundup.d',

-    'bio/sff/index.d',

-    'bio/sff/readrange.d',

-    'bio/sff/reader.d',

-    'bio/sff/constants.d',

-    'bio/sff/read.d',

-    'bio/sff/writer.d',

+    'bio/core/fasta.d',

+    'bio/core/fastq.d',

+    'bio/core/genotype.d',

+    'bio/core/kmer.d',

+    'bio/core/region.d',

+    'bio/core/sequence.d',

+    'bio/core/tinymap.d',

+    'bio/core/utils/algo.d',

+    'bio/core/utils/bylinefast.d',

+    'bio/core/utils/exception.d',

+    'bio/core/utils/format.d',

+    'bio/core/utils/memoize.d',

+    'bio/core/utils/outbuffer.d',

+    'bio/core/utils/range.d',

+    'bio/core/utils/roundbuf.d',

+    'bio/core/utils/stream.d',

+    'bio/core/utils/switchendianness.d',

+    'bio/core/utils/tmpfile.d',

+    'bio/core/utils/zlib.d',

+    'bio/maf/block.d',

+    'bio/maf/parser.d',

+    'bio/maf/reader.d',

+    'bio/sam/header.d',

+    'bio/sam/reader.d',

     'bio/sam/utils/fastrecordparser.d',

     'bio/sam/utils/recordparser.d',

-    'bio/sam/reader.d',

-    'bio/sam/header.d'

+    'bio/sff/constants.d',

+    'bio/sff/index.d',

+    'bio/sff/read.d',

+    'bio/sff/reader.d',

+    'bio/sff/readrange.d',

+    'bio/sff/utils/roundup.d',

+    'bio/sff/writer.d'

+]

 

 bio2_src = [

     'bio2/bam/header.d',

@@ -114,18 +121,16 @@

 # Library and pkg-config

 #

 biod_lib = library('biod',

-        include_directories: [src_dir],

         [biod_src, bio2_src],

         dependencies: [undead_dep, zlib_dep],

         install: true,

-        version: project_version,

+        version: meson.project_version(),

         soversion: project_soversion

 )

 pkgc.generate(name: 'biod',

               libraries: biod_lib,

-              subdirs: 'd/',

-              version: project_version,

               subdirs: 'd/bio/',

+              version: meson.project_version(),

               description: 'Bioinformatics library in D (utils for working with SAM, BAM, SFF formats).'

 )

 

@@ -134,11 +139,9 @@

 #

 biod_test_exe = executable('biod_test',

     ['test/unittests.d',

-    biod_src],

-    include_directories: [src_dir],

      biod_src,

      bio2_src],

     dependencies: [undead_dep, zlib_dep],

-    d_args: meson.get_compiler('d').unittest_args()

+    d_unittest: true

 )

 test('biod_tests', biod_test_exe)

debian/patches/fix_clean_target.patch

+4 −0
Original line number Diff line number Diff line 
Author: Andreas Tille <tille@debian.org>

Last-Update: Tue, 19 Mar 2019 09:18:43 +0100

Description: Do not fail if file to be removed does not exist



--- a/Makefile

+++ b/Makefile

@@ -42,5 +42,5 @@ check: $(BIN)