Usage

Streaming Pileupy is meant to be run through its command line interface spileup. Given a sam file in.sam:

@HD VN:1.6  SO:unknown
@SQ SN:chr1 LN:1000000
@RG ID:0    SM:sample_0
@RG ID:1    SM:sample_1
r0  0   chr1    24  0   1M  *   0   0   G   I   RG:Z:0
r1  0   chr1    24  0   1M  *   0   0   G   I   RG:Z:1

, and a sample name file sample_names.txt:

sample_0
sample_1

To run a pileup of the reads in in.sam for the samples in sample_names.txt, run the command:

spileup input.sam sample_names.txt