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.cru...@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 <j...@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 <moel...@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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