on mips/mipsel.
Could you please consider including these changes
in order to build since for mips/mipsel architectures?
Thanks
Aleksandar Zlicic
Index: since-1.1/since.c
===
--- since-1.1.orig/since.c 2014-04-03 14:01:50.0 +
in SAM format.
Attached patch fixes this issue.
It is tested on mips, mipsel and powerpc.
Best Regards
Aleksandar Zlicic
--- a/io_lib/bam.c
+++ b/io_lib/bam.c
@@ -1636,7 +1636,7 @@
/* The remainder, word aligned */
blk_size = blk_ret;
-if ((blk_ret = bam_read(b, (char *)bam_cigar(bs
and mipsel.
This is fixed in '02-fix-alignment.patch'.
With these patches applied I have successfully built htslib on mips/mipsel.
Could you please consider including this patch?
Best regards,
Aleksandar Zlicic
--- a/cram/cram_encode.c
+++ b/cram/cram_encode.c
@@ -1858,6 +1858,12 @@
return rg
Sure, I will upload the patches.
I am currently working on adapting the changes to the latest upstream version.
Also I have added a minor change to patch '02-fix-alignment.patch',
which you will find attached.
Best Regards
Aleksandar Zlicic
Index: htslib-0.2.0~rc3/sam.c
in python-pysam (its output is compared with output from
pysam python module), but samtools has both unaligned memory access
and system endianness issues.
I have attached patches that fix this. With these patches applied to samtools,
python-pysam builds fine.
Best Regards
Aleksandar Zlicic
Index
and mipsel.
Could you consider including these patches?
Best regards,
Aleksandar Zlicic
Index: python-pysam-0.7.7/samtools/bam_import.c.pysam.c
===
--- python-pysam-0.7.7.orig/samtools/bam_import.c.pysam.c
+++ python-pysam-0.7.7
Ok, I will contact upstream.
Best Regards
Aleksandar Zlicic
From: Charles Plessy [ple...@debian.org]
Sent: Wednesday, July 02, 2014 3:16 PM
To: Aleksandar Zlicic; 753...@bugs.debian.org
Subject: Re: [Debian-med-packaging] Bug#753485: samtools: python-pysam
; i n*Bsize; i += 4)
Changes in fix_alignment.patch are to avoid unaligned memory access for
architectures that don't allow it.
I am currently adapting changes to the latest version of samtools. When I'm
done I will contact upstream.
Best Regards
Aleksandar Zlicic
this
experimental branch haven't been merged to the main branch yet.
Best Regards
Aleksandar Zlicic
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