Bryan Lajoie

support for non-amazonaws endpoint urls (e.g. s3.<company>.com)

15

We are utilizing EMC on-premise s3-compatible storage. Htslib does not accommodate non (.s3.amazonaws.com) endpoint urls. We can successfully modify, re-compile and use htslib/samtools if we swap in our own endpoint...

bgzip/tabix bedpe indexing (2D queries)

1

Hi, I was wondering if there has been any discussion around extending bgzip/tabix to support BEDPE files (to ultimately achieve 2D block-compression + retrieval). Useful for Hi-C interaction matrices, SV...

slow access to s3 resources (initial 3-4s lag)

2

Hi, We've noticed that samtools/htslib seems to have a small time penalty when making an initial connection to any s3 resource (local s3 or amazonaws s3). e.g. 1-2 second delay...

C2ORF15 vs C2orf15

1

We (@vgainullin) have found an occurrence of case-sensitive gene names? http://exac.broadinstitute.org/gene/ENSG00000273045 http://exac.broadinstitute.org/gene/ENSG00000241962 Both of these GENES exist in the fordist_cleaned_exac_r03_march16_z_pli_rec_null_data.txt.gz dump. C2ORF15 looks to be invalid. Perhaps this is a...