Hi Aníbal,
thanks for the NMU which is welcome. The only thing I would like you to
do is to commit the changes to VCS. Any DD has commit permision so all
people who can upload can also commit the changes. This time I did fetched
the package source and committed to SVN.
Kind regards and thanks again
Andreas.
On Tue, Apr 01, 2014 at 09:46:29PM +1100, Aníbal Monsalve Salazar wrote:
> debdiff staden-io-lib_1.13.5-1.dsc staden-io-lib_1.13.5-1.1.dsc
> diff -Nru staden-io-lib-1.13.5/debian/changelog
> staden-io-lib-1.13.5/debian/changelog
> --- staden-io-lib-1.13.5/debian/changelog 2014-03-15 03:07:55.000000000
> +0000
> +++ staden-io-lib-1.13.5/debian/changelog 2014-04-01 04:20:39.000000000
> +0100
> @@ -1,3 +1,13 @@
> +staden-io-lib (1.13.5-1.1) unstable; urgency=medium
> +
> + * Non-maintainer upload.
> + * Fix io_lib/bam.c read
> + Patch by Aleksandar Zlicic
> + Add fix-bam-read.patch
> + Closes: #736565
> +
> + -- Anibal Monsalve Salazar <ani...@debian.org> Tue, 01 Apr 2014 04:19:52
> +0100
> +
> staden-io-lib (1.13.5-1) unstable; urgency=medium
>
> * New upstream release.
> diff -Nru staden-io-lib-1.13.5/debian/patches/fix-bam-read.patch
> staden-io-lib-1.13.5/debian/patches/fix-bam-read.patch
> --- staden-io-lib-1.13.5/debian/patches/fix-bam-read.patch 1970-01-01
> 01:00:00.000000000 +0100
> +++ staden-io-lib-1.13.5/debian/patches/fix-bam-read.patch 2014-04-01
> 04:19:23.000000000 +0100
> @@ -0,0 +1,36 @@
> +Date: Mon, 31 Mar 2014 19:22:13 +0200
> +From: Aleksandar Zlicic <aleksandar.zli...@imgtec.com>
> +Subject: staden-io-lib: fix io_lib/bam.c read
> +
> +https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=736565
> +
> +We have fixed a bug reported for the staden-io-lib package
> +(https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=736565). The cause
> +of this problem is an error in function bam_get_seq(), or to be more
> +precise, function's implementation for non-intel architectures.
> +
> +Function bam_get_seq is used for reading data from alignment blocks in
> +BAM files, block by block.
> +
> +In special cases, when the alignment block being read is the last
> +block in BAM file, and the block has no cigar operations and segment
> +sequence stored inside of it, function incorrectly detects
> +end-of-file.
> +
> +In that case, block has actually been successfully read, but because
> +of erroneous end-of-file detection, it isn't written to output file in
> +SAM format.
> +
> +Attached patch fixes this issue.
> +
> +--- a/io_lib/bam.c 2014-01-07 17:01:12.000000000 +0000
> ++++ bio_lib//bam.c 2014-04-01 04:05:16.762660873 +0100
> +@@ -1635,7 +1635,7 @@ int bam_get_seq(bam_file_t *b, bam_seq_t
> +
> + /* The remainder, word aligned */
> + blk_size = blk_ret;
> +- if ((blk_ret = bam_read(b, (char *)bam_cigar(bs), blk_size+4)) == 0)
> ++ if (((blk_ret = bam_read(b, (char *)bam_cigar(bs), blk_size+4)) == 0)
> && blk_size != 0)
> + return 0;
> + if (blk_size+4 != blk_ret) {
> + if (blk_size != blk_ret) {
> diff -Nru staden-io-lib-1.13.5/debian/patches/series
> staden-io-lib-1.13.5/debian/patches/series
> --- staden-io-lib-1.13.5/debian/patches/series 2014-03-11
> 23:05:36.000000000 +0000
> +++ staden-io-lib-1.13.5/debian/patches/series 2014-04-01
> 04:17:07.000000000 +0100
> @@ -1 +1,2 @@
> pathmax.patch
> +fix-bam-read.patch
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