[med-svn] [bwa] 04/07: Remove patches that are not applied
Andreas Tille
tille at debian.org
Mon Nov 13 14:36:00 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository bwa.
commit 19371dc965a288d0c2a736d3a6b1a3325de83e0f
Author: Andreas Tille <tille at debian.org>
Date: Mon Nov 13 15:31:20 2017 +0100
Remove patches that are not applied
---
debian/patches/check_for_nan.patch | 19 ------------
debian/patches/check_number_of_arguments.patch | 16 ----------
debian/patches/print_unsigned_counts.patch | 42 --------------------------
debian/patches/series | 4 ---
debian/patches/spelling.patch | 15 ---------
5 files changed, 96 deletions(-)
diff --git a/debian/patches/check_for_nan.patch b/debian/patches/check_for_nan.patch
deleted file mode 100644
index a02175d..0000000
--- a/debian/patches/check_for_nan.patch
+++ /dev/null
@@ -1,19 +0,0 @@
-Author: Fabian Klötzl
-Description: check computed avg and std for nan
-Last-Update: 2017-07-03
-Bug: https://github.com/lh3/bwa/issues/108
-===========================================================
-Index: bwa/bwtsw2_pair.c
-===================================================================
---- bwa.orig/bwtsw2_pair.c
-+++ bwa/bwtsw2_pair.c
-@@ -91,6 +91,9 @@ bsw2pestat_t bsw2_stat(int n, bwtsw2_t *
- if (r.high < r.avg + MAX_STDDEV * r.std) r.high = (int)(r.avg + MAX_STDDEV * r.std + .499);
- ksprintf(msg, "[%s] low and high boundaries for proper pairs: (%d, %d)\n", __func__, r.low, r.high);
- free(isize);
-+ if (isnan(r.avg) || isnan(r.std)){
-+ r.failed = 1;
-+ }
- return r;
- }
-
diff --git a/debian/patches/check_number_of_arguments.patch b/debian/patches/check_number_of_arguments.patch
deleted file mode 100644
index 46a8c8f..0000000
--- a/debian/patches/check_number_of_arguments.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Sun, 12 Jul 2015 14:59:23 +0200
-Bug-Debian: http://bugs.debian.org/715703
-Description: Check exact number of arguments of bwtupdate
-
---- a/bwtindex.c
-+++ b/bwtindex.c
-@@ -152,7 +152,7 @@ void bwt_bwtupdate_core(bwt_t *bwt)
- int bwa_bwtupdate(int argc, char *argv[]) // the "bwtupdate" command
- {
- bwt_t *bwt;
-- if (argc < 2) {
-+ if (argc != 2) {
- fprintf(stderr, "Usage: bwa bwtupdate <the.bwt>\n");
- return 1;
- }
diff --git a/debian/patches/print_unsigned_counts.patch b/debian/patches/print_unsigned_counts.patch
deleted file mode 100644
index c9aa6aa..0000000
--- a/debian/patches/print_unsigned_counts.patch
+++ /dev/null
@@ -1,42 +0,0 @@
-Author: Fabian Klötzl
-Description: change printing as size_t is unsigned
-Last-Update: 2017-07-03
-===========================================================
---- bwa.orig/malloc_wrap.c
-+++ bwa/malloc_wrap.c
-@@ -13,7 +13,7 @@
- void *p = calloc(nmemb, size);
- if (NULL == p) {
- fprintf(stderr,
-- "[%s] Failed to allocate %zd bytes at %s line %u: %s\n",
-+ "[%s] Failed to allocate %zu bytes at %s line %u: %s\n",
- func, nmemb * size, file, line, strerror(errno));
- exit(EXIT_FAILURE);
- }
-@@ -25,7 +25,7 @@
- void *p = malloc(size);
- if (NULL == p) {
- fprintf(stderr,
-- "[%s] Failed to allocate %zd bytes at %s line %u: %s\n",
-+ "[%s] Failed to allocate %zu bytes at %s line %u: %s\n",
- func, size, file, line, strerror(errno));
- exit(EXIT_FAILURE);
- }
-@@ -37,7 +37,7 @@
- void *p = realloc(ptr, size);
- if (NULL == p) {
- fprintf(stderr,
-- "[%s] Failed to allocate %zd bytes at %s line %u: %s\n",
-+ "[%s] Failed to allocate %zu bytes at %s line %u: %s\n",
- func, size, file, line, strerror(errno));
- exit(EXIT_FAILURE);
- }
-@@ -49,7 +49,7 @@
- char *p = strdup(s);
- if (NULL == p) {
- fprintf(stderr,
-- "[%s] Failed to allocate %zd bytes at %s line %u: %s\n",
-+ "[%s] Failed to allocate %zu bytes at %s line %u: %s\n",
- func, strlen(s), file, line, strerror(errno));
- exit(EXIT_FAILURE);
- }
diff --git a/debian/patches/series b/debian/patches/series
index db1efa1..43d7dc4 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,6 +1,2 @@
-#print_unsigned_counts.patch # adopted upstream
-#check_for_nan.patch # Superseeded by upstream bcb475cd033b3641d2de19ad6fb70da7bdd54f77
fix_heap_block_overrun # See https://github.com/lh3/bwa/issues/146
fix_build_on_freebsd.patch
-#check_number_of_arguments.patch # adopted upstream
-#spelling.patch # adopted upstream
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
deleted file mode 100644
index 5d8b73e..0000000
--- a/debian/patches/spelling.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Sun, 12 Jul 2015 14:59:23 +0200
-Description: Fix spelling
-
---- a/fastmap.c
-+++ b/fastmap.c
-@@ -259,7 +259,7 @@ int main_mem(int argc, char *argv[])
- fprintf(stderr, " -E INT[,INT] gap extension penalty; a gap of size k cost '{-O} + {-E}*k' [%d,%d]\n", opt->e_del, opt->e_ins);
- fprintf(stderr, " -L INT[,INT] penalty for 5'- and 3'-end clipping [%d,%d]\n", opt->pen_clip5, opt->pen_clip3);
- fprintf(stderr, " -U INT penalty for an unpaired read pair [%d]\n\n", opt->pen_unpaired);
-- fprintf(stderr, " -x STR read type. Setting -x changes multiple parameters unless overriden [null]\n");
-+ fprintf(stderr, " -x STR read type. Setting -x changes multiple parameters unless overridden [null]\n");
- fprintf(stderr, " pacbio: -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0 (PacBio reads to ref)\n");
- fprintf(stderr, " ont2d: -k14 -W20 -r10 -A1 -B1 -O1 -E1 -L0 (Oxford Nanopore 2D-reads to ref)\n");
- fprintf(stderr, " intractg: -B9 -O16 -L5 (intra-species contigs to ref)\n");
--
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