Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.
Hi.
I am using igv-reports python package to generate igv pictures for the given sample located on s3 but it crushes on the part where it uses pysam package showing protocol not supported.
I tried to just use pysam.view but it also crushed with exit code 1 and again showed can't open file protocol not supported.
I thought that it is because of the samtools installed in my environment in Kubernetes cause the samtools in there gives the same error.
So I decided to use all of it locally with satmools version 1.18 with htslib version 1.18 but it didn't worked.
Also I searched in several packages to see where the samtools directory is located but haven't found any.
Hi. I am using igv-reports python package to generate igv pictures for the given sample located on s3 but it crushes on the part where it uses pysam package showing protocol not supported. I tried to just use pysam.view but it also crushed with exit code 1 and again showed can't open file protocol not supported. I thought that it is because of the samtools installed in my environment in Kubernetes cause the samtools in there gives the same error. So I decided to use all of it locally with satmools version 1.18 with htslib version 1.18 but it didn't worked. Also I searched in several packages to see where the samtools directory is located but haven't found any.
Is there any way to use pysam with s3 files ?