update install of rjson

v2.0.4

Update Dockerfile

reduce uninformative output

This release contains an update to run.sh that omits the "--show-progress" parameter to sambama sort, which generates many uninformative lines of output.

Dockerfile specifies Python 2.7.14; tidyverse rollback

That's it. That's the release.

Supports alternative genome and gene models

This release was used to build the docker ucsctreehouse/bam-mend-qc:2.0.0.

This release can accept a third parameter to specify the bed file used to identify exons, allowing people to use it with alternative genome and gene models. If no bed file is specified, the default included bed file (hg38; gencode 23) is used.

Also:
Refactored/modernized the code in parseReadDist.R
Changed docker and output file names to conform with MEND
Changed column/field names in output to be more intuitive
Specified all libraries in requirements.txt; the resulting Docker container fails otherwise

Used in Treehouse production 2018-present

This code was used to generate ucsctreehouse/bam-umend-qc:1.1.1
(DIGEST:sha256:f1e094f84c210e65ab04a24812b49d865091c50d0a90d66c004516bce7e17961), available at https://hub.docker.com/r/ucsctreehouse/bam-umend-qc.

It can be run as follows:

	docker run --rm \
	  -v `pwd`/$(shell find outputs/expression/*.bam):/inputs/sample.bam \
		-v $(shell pwd)/outputs/qc:/tmp \
		-v $(shell pwd)/outputs/qc:/outputs \
		ucsctreehouse/bam-umend-qc@sha256:5f286d72395fcc5085a96d463ae3511554acfa4951aef7d691bba2181596c31f \
			/inputs/sample.bam /outputs