On 14 May 2015, at 22:02, Heng Li <l...@me.com> wrote:
> A historical background. Terminating at EOF was intended initially. The idea
> was to allow a BAM footer for extra information, such as the index.
> Nonetheless, we have not gone much further with this idea.
Emails of the time [1] suggest it was floated as an idea fairly early rather
than "intended initially". I continue to think [2] it would have been a
mistake to signal EOF solely at the BGZF "transport layer" and not at the BAM
format layer (e.g. with a terminator alignment record with block_size=0).
As you say, this idea never gained much traction. Appending does seem to be
gaining traction. While it would be possible to remove soon-to-be-nonfinal EOF
blocks by concatenating in a fancy way that truncated 28 bytes from the first
file when it has an EOF block, this is incompatible with using the ordinary
cat(1) command or opening files with "a" / O_APPEND -- or with some easy piping
-- so can't be relied on.
We do have a program here to remove EOF blocks to facilitate catting, and could
probably add such a tool to htslib or so.
John
[1] http://sourceforge.net/p/samtools/mailman/message/23665824/
[2] http://sourceforge.net/p/samtools/mailman/message/23666383/
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