[Samtools-help] samtools do not validate uncompressed BAM file

[Soboleva, A. (NIH/N. [E] <sob...@nc...>]

Dear samtools developers,

We encountered the following problem.

We received uncompressed BAM file as a part of submission to GEO database

When we tried to validate it with "samtools view -H", there was error message

[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[main_samview] fail to read the header from "GSM721162_1b.bam".

After I compressed file with bgzip, I was able to read its header.
According to documentation, samtools are able to read input file either
compressed or uncompressed.


samtools versions tried: 0.1.15 and 0.1.18


Thanks for looking into it!


Alexandra Soboleva
GEO group software developer lead
NCBI/NLM/NIH