Hi Eric,
There has been a long-running difference of opinion on topics like this, with
one group pushing the view that is in the spec (i.e. behaviour like this should
be left unspecified) and there’s another group (including me) that believes
that SAM & BAM are complex enough formats and so many mistakes are made
creating BAM files that it is better to test for situations like this as they
most likely indicate an error, perhaps one of consequence, somewhere earlier in
the processing chain.
If you would prefer to ignore this error with ValidateSamFile you can
selectively ignore validations you find too strict with the IGNORE= option.
-t
On Sep 12, 2014, at 2:22 AM, Eric Roller <[email protected]> wrote:
> Using version 1.119 I get this error:
>
> First of pair flag should not be set for unpaired read
>
> Basically, Picard is complaining that 0x40 is set when 0x1 is unset. However,
> from the samtools specification:
> "If 0x1 is unset, no assumptions can be made about 0x2, 0x8, 0x20, 0x40 and
> 0x80."
>
> Furthermore, the 0x40 description from the spec says
> 0x40 the first segment in the template
> For an unpaired read it will be both the first and last segment in the
> template. That doesn't mean it is paired so there should be no error here.
>
> Am I missing something?
>
> Thanks,
> --
> Eric Roller
> ------------------------------------------------------------------------------
> Want excitement?
> Manually upgrade your production database.
> When you want reliability, choose Perforce
> Perforce version control. Predictably reliable.
> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk_______________________________________________
> Samtools-help mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/samtools-help
------------------------------------------------------------------------------
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
_______________________________________________
Samtools-help mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/samtools-help
