Tags: cancerit/BRASS

Change bedtools due to errors in subsets of data, fix version of gam …

…due to recent lib (R) change

singularity edgecase, likely due to change in pcap-core base image

FInliase fix to deploy following CI checks

Fixes #95

Ass supported docker standalone container

Fixes for #85 and #86

Fixes a problem with RGID=0 and slightl improvement to speed of input

* Fixed bug where subset of intervals does not have reads -issue#65

* Informative error when .bas file is absent - issue#71
* temp file were now kept after running filter step - issue#73
* Fixed issue#66
* Added script to process centro/telomere data - issue#70
* Fixed bug where intermediate file name matches with one of the sample

* Change tabix->query to tabix->query_full

Handle the full flow correctly when CRAM is input or BAM+CSI indexes