htsget-refserver-utils

Helper utilities for the htsget reference server

https://img.shields.io/coveralls/github/ga4gh/htsget-refserver-utils?style=flat-square

Installation

Clone repo and build from source:

git clone https://github.com/ga4gh/htsget-refserver-utils.git
cd htsget-refserver-utils
go build -o ./htsget-refserver-utils .
./htsget-refserver-utils

Install binary to $GOBIN:

go get -u "github.com/ga4gh/htsget-refserver-utils"
go install "github.com/ga4gh/htsget-refserver-utils"
htsget-refserver-utils

Usage

htsget-refserver-utils contains multiple subcommands that can be specified on command line, i.e.

htsget-refserver-utils ${SUBCOMMAND} ${ARG1} ${ARG2} ... ${ARGN}

Subcommands

• modify-sam
  • streams a SAM file from stdin, emitting custom fields and tags to stdout
  • ex: htsget-refserver-utils modify-sam -fields QNAME,FLAG -tags NM,MD -notags HI
• help
  • prints help message

Testing

Run all tests

go test ./...

Run all tests and produce coverage report

go test ./... -coverprofile=cp.out