[Debian-med-packaging] Bug#877670: Bug#877670: bcftools FTBFS on armel armhf and ppc64el

[Graham Inggs]

On 14 October 2017 at 03:12, peter green <plugwash at p10link.net> wrote:
> Here is the diff I got on my armhf system.
>
> --- test/mpileup/indel-AD.1.out 2017-06-20 11:49:44.000000000 +0000
> +++ test/mpileup/indel-AD.1.out.new     2017-10-14 01:06:23.687285852 +0000
> @@ -154,7 +154,7 @@
>  000000F        524     .       T       G,<*>   0       .
> DP=119;I16=64,44,1,0,4253,180647,27,729,6480,388800,60,3600,2460,59296,25,625;QS=0.993531,0.00646862,0;SGB=-0.379885;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0
> PL:AD   0,255,255,255,255,255:108,1,0
>  000000F        525     .       A       <*>     0       .
> DP=119;I16=63,39,0,0,4126,179608,0,0,6120,367200,0,0,2330,56198,0,0;QS=1,0;MQSB=1;MQ0F=0
> PL:AD   0,255,255:102,0
>  000000F        526     .       T       <*>     0       .
> DP=120;I16=62,45,0,0,4234,181460,0,0,6420,385200,0,0,2450,58910,0,0;QS=1,0;MQSB=1;MQ0F=0
> PL:AD   0,255,255:107,0
> -000000F        527     .       C       <*>     0       .
> DP=120;I16=64,40,0,0,4275,186993,0,0,6240,374400,0,0,2382,57234,0,0;QS=1,0;MQSB=1;MQ0F=0
> PL:AD   0,255,255:104,0
> +000000F        527     .       C       <*>     0       .
> DP=120;I16=64,40,0,0,4275,186993,0,0,6240,374400,0,0,2382,57234,0,0;QS=1,0;MQSB=1;MQ0F=0
> PL:AD   0,255,0:104,0
>  000000F        528     .       A       <*>     0       .
> DP=121;I16=62,45,0,0,4346,189994,0,0,6420,385200,0,0,2426,58030,0,0;QS=1,0;MQSB=1;MQ0F=0
> PL:AD   0,255,255:107,0
>  000000F        529     .       T       <*>     0       .
> DP=123;I16=64,43,0,0,4397,193617,0,0,6420,385200,0,0,2439,58361,0,0;QS=1,0;MQSB=1;MQ0F=0
> PL:AD   0,255,255:107,0
>  000000F        530     .       G       <*>     0       .
> DP=123;I16=66,42,0,0,4392,192268,0,0,6480,388800,0,0,2486,59400,0,0;QS=1,0;MQSB=1;MQ0F=0
> PL:AD   0,255,255:108,0

Thanks!

This failure reminds me of #865060, which failed on architectures
where char is unsigned by default.
Reverting upstream's commit 'Fix mpileup's incorrect FMT/AD indel
depths' [1] avoids the FTBFS, but that doesn't necessarily mean the
bug is in that commit.  I'll dig further when I have a chance.

[1] https://github.com/samtools/bcftools/commit/3c1205c12b3854912c9a6dfe4b214524ea07f12a