[med-svn] [bcftools] 03/05: Refresh patches for new upstream version, removed unused patches
Andreas Tille
tille at debian.org
Mon Dec 11 14:37:20 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository bcftools.
commit 7d3f4ad6614157aecf8c5f088dee71cd5efd9df4
Author: Andreas Tille <tille at debian.org>
Date: Mon Dec 11 13:28:13 2017 +0100
Refresh patches for new upstream version, removed unused patches
---
debian/changelog | 7 +++++++
debian/patches/compiler-flags.patch | 22 --------------------
debian/patches/external-libs.patch | 39 -----------------------------------
debian/patches/series | 3 ---
debian/patches/spelling.patch | 33 -----------------------------
debian/patches/tests-pluginpath.patch | 2 +-
6 files changed, 8 insertions(+), 98 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index f8bd1c4..f799b46 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+bcftools (1.6-1) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * New upstream version
+
+ -- Andreas Tille <tille at debian.org> Mon, 11 Dec 2017 13:26:17 +0100
+
bcftools (1.5-4) unstable; urgency=medium
* Team upload.
diff --git a/debian/patches/compiler-flags.patch b/debian/patches/compiler-flags.patch
deleted file mode 100644
index 0912d02..0000000
--- a/debian/patches/compiler-flags.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-Description: Allow compiler flags to be passed through to build system
- The development version of the upstream code already supports LDFLAGS,
- so many parts of this patch will not be needed in the next upstream
- release
-Author: Afif Elghraoui <afif at ghraoui.name>
-Forwarded: not-needed
-Last-Update: 2015-11-09
---- a/config.mk.in
-+++ b/config.mk.in
-@@ -34,9 +34,9 @@ bindir = @bindir@
- datarootdir = @datarootdir@
- mandir = @mandir@
-
--CC = @CC@
--CPPFLAGS = @CPPFLAGS@
--CFLAGS = @CFLAGS@
-+CC ?= @CC@
-+CPPFLAGS ?=
-+CFLAGS += @CFLAGS@
- LDFLAGS ?=
- LIBS = $(LDFLAGS) -lhts
-
diff --git a/debian/patches/external-libs.patch b/debian/patches/external-libs.patch
deleted file mode 100644
index 3aaf337..0000000
--- a/debian/patches/external-libs.patch
+++ /dev/null
@@ -1,39 +0,0 @@
-Description: Use packaged libraries
-Author: Afif Elghraoui <afif at ghraoui.name>
-Forwarded: not-needed
-Last-Update: 2015-11-03
---- a/config.mk.in
-+++ b/config.mk.in
-@@ -37,27 +37,21 @@ mandir = @mandir@
- CC = @CC@
- CPPFLAGS = @CPPFLAGS@
- CFLAGS = @CFLAGS@
--LDFLAGS = @LDFLAGS@
--LIBS = @LIBS@
-+LDFLAGS ?=
-+LIBS = $(LDFLAGS) -lhts
-
- DYNAMIC_FLAGS = @CC_RDYNAMIC_OPT@
-
- USE_GPL = @USE_GPL@
--GSL_LIBS = @GSL_LIBS@
-+GSL_LIBS = -lgsl -lgslcblas
-
- PLATFORM = @PLATFORM@
- PLUGINS_ENABLED = @enable_bcftools_plugins@
- plugindir = @bcf_plugindir@
- PLUGIN_EXT = @PLUGIN_EXT@
-
-- at Hsource@HTSDIR = @HTSDIR@
-- at Hsource@include $(HTSDIR)/htslib.mk
-- at Hsource@include $(HTSDIR)/htslib_static.mk
-- at Hsource@HTSLIB = $(HTSDIR)/libhts.a
-- at Hsource@HTSLIB_LIB = $(HTSLIB) $(HTSLIB_static_LIBS)
-- at Hsource@HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS)
-- at Hsource@BGZIP = $(HTSDIR)/bgzip
-- at Hsource@TABIX = $(HTSDIR)/tabix
-+ at Hsource@BGZIP = /usr/bin/bgzip
-+ at Hsource@TABIX = /usr/bin/tabix
- HTSLIB_CPPFLAGS = @HTSLIB_CPPFLAGS@
- @Hinstall at HTSLIB_LDFLAGS = @HTSLIB_LDFLAGS@
- @Hinstall at HTSLIB_LIB = -lhts
diff --git a/debian/patches/series b/debian/patches/series
index a6429f0..450663e 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,6 +1,3 @@
-# external-libs.patch
-# compiler-flags.patch
-# destdir.patch
tests-pluginpath.patch
test-regidx-unsigned-char.patch
fix-test_vcf_query.patch
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
deleted file mode 100644
index 296c042..0000000
--- a/debian/patches/spelling.patch
+++ /dev/null
@@ -1,33 +0,0 @@
-Description: Fix spelling errors
-Author: Afif Elghraoui <afif at ghraoui.name>
-Forwarded: no
-Last-Update: 2015-11-09
---- bcftools.orig/doc/bcftools.1
-+++ bcftools/doc/bcftools.1
-@@ -546,7 +546,7 @@
- .RE
- .SS "bcftools annotate \fI[OPTIONS]\fR \fIFILE\fR"
- .sp
--This command allows to add or remove annotations\&.
-+This command allows one to add or remove annotations\&.
- .PP
- \fB\-a, \-\-annotations\fR \fIfile\fR
- .RS 4
-@@ -1041,7 +1041,7 @@
- likelihood of novel mutation for constrained
- \fB\-C\fR
- \fItrio\fR
--calling\&. The trio genotype calling maximizes likelihood of a particular combination of genotypes for father, mother and the child P(F=i,M=j,C=k) = P(unconstrained) * Pn + P(constrained) * (1\-Pn)\&. By providing three values, the mutation rate Pn is set explictly for SNPs, deletions and insertions, respectively\&. If two values are given, the first is interpreted as the mutation rate of SNPs and the second is used to calculate the mutation rate of indels according to their length as P [...]
-+calling\&. The trio genotype calling maximizes likelihood of a particular combination of genotypes for father, mother and the child P(F=i,M=j,C=k) = P(unconstrained) * Pn + P(constrained) * (1\-Pn)\&. By providing three values, the mutation rate Pn is set explicitly for SNPs, deletions and insertions, respectively\&. If two values are given, the first is interpreted as the mutation rate of SNPs and the second is used to calculate the mutation rate of indels according to their length as [...]
- .RE
- .PP
- \fB\-p, \-\-pval\-threshold\fR \fIfloat\fR
-@@ -2512,7 +2512,7 @@
- // Longer description used by \*(Aqbcftools +name \-h\*(Aq
- const char *usage(void);
-
--// Called once at startup, allows to initialize local variables\&.
-+// Called once at startup, allows one to initialize local variables\&.
- // Return 1 to suppress normal VCF/BCF header output, \-1 on critical
- // errors, 0 otherwise\&.
- int init(int argc, char **argv, bcf_hdr_t *in_hdr, bcf_hdr_t *out_hdr);
diff --git a/debian/patches/tests-pluginpath.patch b/debian/patches/tests-pluginpath.patch
index 4049da5..e413aec 100644
--- a/debian/patches/tests-pluginpath.patch
+++ b/debian/patches/tests-pluginpath.patch
@@ -10,7 +10,7 @@ Forwarded: not-needed
Last-Update: 2015-11-09
--- a/test/test.pl
+++ b/test/test.pl
-@@ -862,7 +862,7 @@ sub test_vcf_plugin
+@@ -885,7 +885,7 @@ sub test_vcf_plugin
{
my ($opts,%args) = @_;
if ( !$$opts{test_plugins} ) { return; }
--
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