[Samtools-devel] samtools pileup bug when using unix soft link as reference fasta

[Henry B. <hrb...@gm...>]

hi,

  i wanted to alert people to a bug in samtools pileup.  i had been noticing
that every once in awhile, one of many pileup files i had produced had 'N'
as the reference, even though i'd used the -f ref.fasta option in samtools
pileup (0.1.7a).  and consequently, the pileup line shows a lot of one
nucleotide, rather than dots and commas.

aaron berlin thankfully alerted me to the fact that this only occurs when
the fasta file is a UNIX link (i think just soft link, i haven't tried it
with hard links).  and, in running it 24 times, all with different soft link
fasta references, only two of the pileups showed 'N' in the reference
column.

if time permits and i can spot the cause, i'll try to submit a patch.

thanks,

henry