[ensembl-dev] Rendering deletions in BAM files

[Fedor Gusev]

Cigar string: 15M23D86M

Here is the extract from our BAM file:
HWI-ST150_0130:8:22:1406:191742#0       163     1       924162  70
 15M23D86M       =       924458  396
CTGGAGTTCAGGGTTGAGTGTTTCGGGAGTTCTGGGTTGATTGTTTCTNGGGTTCAGGGTTGATTGTTTCTGGAGTTCAGGGTTGATTATTTCTGGTGTTT
 =EFHCF<@F>FFF=@FAG=F>@@F<EEAF=?EDFEE=@F@@@E=@@AC*@<A;><>CEE<?E<=><:??5EB<@F=?2*8972:6<;=6.??=0-(---,*
 X0:i:1  X1:i:0  OC:Z:101M       RG:Z:S000007    XG:i:0  AM:i:37
NM:i:25 SM:i:37 XM:i:4  XO:i:0  OP:i:924185   MQ:i:60
OQ:Z:ffffffdffffffeffcfdfefffceebebeeededdff`fecceb``Ba[aYa\aaddacbY\`XYaaVd^\`daaTKT[WMYS[Y^UK``^BBBBBBBB
     XT:A:U

Attached are renders from Ensembl (with and without patch) and the
same read rendered by IGV.

On Wed, Aug 31, 2011 at 7:36 AM, Steve Searle <searle at sanger.ac.uk> wrote:
> Hi Fedor
>
> I'm looking at your patch. Could you send me some examples of cigar strings
> you think are being handled wrong, or a very small test bam file, to allow
> me to reproduce the problem.
>
> Thanks and Regards
>
> Steve
>
> On 30 Aug 2011, at 09:06, Fedor Gusev wrote:
>
>> Hello.
>>
>> I think BAM rendering code has an error. Basically, the cigar string
>> is threated the wrong way. It has the form ([0-9]*[MDISN])* while code
>> assumes ([MDISN][0-9]*)* . This results in everything being threated
>> as match and no deletions are shown.
>>
>> Attach patch fixes it.
>>
>> --
>> Kind regards,
>> Fedor Gusev.
>> <bam.patch>_______________________________________________
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>
>
>
> --
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-- 
Kind regards,
Fedor Gusev.
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