score-client fails with view command

[junjun-zhang]

Observed behaviour

Object 1: aligned BAM

The follow view command failed with ERROR: Command error: Cannot query stream-based BAM file

score-client --profile collab view --object-id d98a83e3-1f79-5213-949d-cb79894cb775

But after downloading the object to local, view using samtools works well

samtools view PCAWG.833cdc6c-dd38-11e4-8ffa-a3b5c254ba06.TopHat2.v1.bam | less

Object 2: unaligned BAM

This failed with ERROR: Bad parameter(s): No index file associated with BAM/CRAM file with object id '2e159ade-b18d-5d1a-99cc-9239883e6d1e'

score-client --profile collab view --header-only --object-id 2e159ade-b18d-5d1a-99cc-9239883e6d1e

But samtools view works fine after downloading it.

samtools view -H cf3033d4c0c1388ea3ef4545ad6c1bf0.Sample_00230111_2.bam

Expected behaviour

score-client view command (with or without --header-only option) should work on both aligned and unaligned BAM objects. Slicing BAM using query option like --query 1:1245-1425 will require to have associated BAI index object exist.