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commit 19371dc965a288d0c2a736d3a6b1a3325de83e0f Author: Andreas Tille <[email protected]> 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 <[email protected]> -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 <[email protected]> -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"); -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bwa.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
