[emboss-dev] EMBOSS 6.3.0 released - SAM/BAM

Peter biopython at maubp.freeserve.co.uk
Thu Jul 15 11:01:52 UTC 2010

Trying again, sending from right email address...

---------- Forwarded message ----------
From: Peter <peter at maubp.freeserve.co.uk>
To: ajb at ebi.ac.uk, Peter Rice <pmr at ebi.ac.uk>
Date: Thu, 15 Jul 2010 11:45:21 +0100
Subject: EMBOSS 6.3.0 released - SAM/BAM
On Thu, Jul 15, 2010 at 11:20 AM,  <ajb at ebi.ac.uk> wrote:
> EMBOSS 6.3.0 is now available and can be downloaded from
> our ftp server:

Congratulations on the latest release.

> Some highlights include:
>    ...
>    Support for BAM/SAM files
>    ...

Cool. I should take a look at this before (if) merging SAM/BAM
support into Biopython. The use case I had in mind was for
conversion to FASTQ (discarding any alignment information).

What do you do about naming for paired reads? I was appending
/1 or /2 to match the Illumina convention. Doing nothing means
the paired reads will have the same names.

What do you do about the strand issue? SAM/BAM stored reads
which map onto the reverse strand in reverse complement. If
you want to get back to the original orientation for output as
FASTQ you must apply the reverse complement (plus reverse
the quality scores too of course).

Do you support writing SAM/BAM files? If so, would this be
for aligned reads or unaligned reads only?

Assuming you do write BAM files, do you support the recent
convention to use a single BGZF block, and that where possible
reads should not span a BGZF block boundary?

(I'm assuming some of the EMBOSS team must be on the
samtools-devel mailing list which is where most SAM/BAM
format discussion seems to take place)


Peter C

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