[Samtools-help] memory usage of samtools view -b -S

[Matthias H. <m.h...@md...>]

Hi,

I am trying to convert a 37GB sam file into bam format using samtools 
view -b -S ... I had some trouble with the memory usage which made my 
jobs crash on smaller machines. If I understand correctly sam to bam 
conversion is basically equivalent to compressing the file with bgzip. I 
would expect that the memory usage is constant since data can be 
processed on the fly. However, when I monitored memory usage I saw a 
linear increase up to 10GB. Is this the expected behaviour or is there 
some memory leak in samtools?

Best,
Matthias