[Samtools-devel] samtools view segfaults on SAM with header (0.14)

[Keith J. <kd...@sa...>]

I'm trying out the new 0.1.4 release using the ex1 dataset in the
examples directory.

I can run view sam->bam successfully on the sam file 'as is'. However,
attaching a legal header causes the conversion to segfault.

The following segfault with a legal SAM header

samtools view -b -t ex1.fa.fai ex1.sam.gz
samtools view -S -b -t ex1.fa.fai ex1.sam.gz
samtools view -b -t ex1.fa.fai ex1.sam
samtools view -S -b -t ex1.fa.fai ex1.sam 

The obsolete import function segfaults too.

I'm running X86_64 gcc 4.3.3

The header was imported in version 0.1.3

thanks,

-- 

- Keith James - Wellcome Trust Sanger Institute, UK -


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