[med-svn] [Git][med-team/staden-io-lib][master] 3 commits: debian/patches/s390x: applied patch from upstream to fix big endian builds

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / staden-io-lib


Commits:
c7f8ef45 by Michael R. Crusoe at 2020-05-21T10:57:40+02:00
debian/patches/s390x: applied patch from upstream to fix big endian builds

- - - - -
366a590b by Michael R. Crusoe at 2020-05-21T11:01:06+02:00
usedebianhtscodecs.patch: added DEP-3 metadata

- - - - -
1a246afa by Michael R. Crusoe at 2020-05-21T12:59:41+02:00
debian/upstream/metadata: added repository & bug entries

- - - - -


5 changed files:

- debian/changelog
- + debian/patches/s390x.patch
- debian/patches/series
- debian/patches/usedebianhtscodecs.patch
- debian/upstream/metadata


Changes:

=====================================
debian/changelog
=====================================
@@ -1,12 +1,14 @@
 staden-io-lib (1.14.12-2) UNRELEASED; urgency=medium
 
-  * Team upload.
   * File more spelling typos
   * Install upstream's manual pages
   * include symbols in the package
   * debian/control: fix typo in the package descriptions
   * debian/rules: add hack to autoconf not forget MMAP with cross
     building
+  * debian/patches/s390x: applied patch from upstream to fix big endian builds
+  * debian/patches/usedebianhtscodecs.patch: added DEP-3 patch metadata
+  * debian/upstream/metadata: added repository & bug entries
 
  -- Michael R. Crusoe <michael.crusoe at gmail.com>  Thu, 21 May 2020 10:38:58 +0200
 


=====================================
debian/patches/s390x.patch
=====================================
@@ -0,0 +1,20 @@
+Subject: Fixed big-endian bug in XDELTA codec
+Origin: upstream, https://github.com/jkbonfield/io_lib/commit/8a53a84bd84630ca0964a040d11dad63aa3d2f3e
+From: James Bonfield <jkb at sanger.ac.uk>
+Last-Update: 2020-02-24
+
+---
+ io_lib/cram_codecs.c | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+--- staden-io-lib.orig/io_lib/cram_codecs.c
++++ staden-io-lib/io_lib/cram_codecs.c
+@@ -1482,7 +1482,7 @@
+ 	part = in_size%2;
+ 	if (part) {
+ 	    uint16_t z = in[0];
+-	    c->e_xdelta.last = le_int2(z);
++	    c->e_xdelta.last = z;
+ 	    cp += c->vv->varint_put32(cp, NULL, zigzag16(c->e_xdelta.last));
+ 	}
+ 


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
+s390x.patch
 pathmax.patch
 fix_fseeko.patch
 spelling


=====================================
debian/patches/usedebianhtscodecs.patch
=====================================
@@ -1,5 +1,8 @@
-Index: staden-io-lib/Makefile.am
-===================================================================
+Description: Use the packaged htscodecs library
+Author: Steffen Moeller <moeller at debian.org>
+Forwarded: not-needed
+Last-Updated: 2020-05-20
+
 --- staden-io-lib.orig/Makefile.am
 +++ staden-io-lib/Makefile.am
 @@ -32,7 +32,7 @@
@@ -11,11 +14,9 @@ Index: staden-io-lib/Makefile.am
  
  man_MANS = \
  	man/man1/srf_index_hash.1 \
-Index: staden-io-lib/io_lib/Makefile.am
-===================================================================
 --- staden-io-lib.orig/io_lib/Makefile.am
 +++ staden-io-lib/io_lib/Makefile.am
-@@ -134,6 +134,6 @@ libstaden_read_la_SOURCES = \
+@@ -134,6 +134,6 @@
  	bgzip.h \
  	cram_block_compression.h
  


=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,7 @@
+Repository: https://github.com/jkbonfield/io_lib.git
+Repository-Browse: https://github.com/jkbonfield/io_lib
+Bug-Database: https://github.com/jkbonfield/io_lib/issues
+Bug-Submit: https://github.com/jkbonfield/io_lib/issues/new/choose
 Registry:
  - Name: conda:bioconda
    Entry: staden_io_lib



View it on GitLab: https://salsa.debian.org/med-team/staden-io-lib/-/compare/2205c1c5418af487d7303068e4d78c51aad821dd...1a246afadac51c354eb884fa50fc9961b504e748

-- 
View it on GitLab: https://salsa.debian.org/med-team/staden-io-lib/-/compare/2205c1c5418af487d7303068e4d78c51aad821dd...1a246afadac51c354eb884fa50fc9961b504e748
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