added to README, moved main method to repo root dir for go install co…

…mmand

README.md

@@ -1,12 +1,55 @@
+[![Logo](https://www.ga4gh.org/wp-content/themes/ga4gh-theme/gfx/GA-logo-horizontal-tag-RGB.svg)](https://ga4gh.org)
+
+[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg?style=flat-square)](https://opensource.org/licenses/Apache-2.0)
+[![Go Report](https://goreportcard.com/badge/github.com/ga4gh/htsget-refserver-utils)](https://goreportcard.com/badge/github.com/ga4gh/htsget-refserver-utils)
+[![Travis (.org)](https://img.shields.io/travis/ga4gh/htsget-refserver-utils?style=flat-square)](https://travis-ci.org/ga4gh/htsget-refserver-utils)
+[![Coveralls github](https://img.shields.io/coveralls/github/ga4gh/htsget-refserver-utils?style=flat-square)](https://coveralls.io/github/ga4gh/htsget-refserver-utils?branch=master)
+
 # htsget-refserver-utils
-Helper utilities for the htsget reference server
+Helper utilities for the [htsget reference server](https://github.com/ga4gh/htsget-refserver)
+
+https://img.shields.io/coveralls/github/ga4gh/htsget-refserver-utils?style=flat-square
 
-## Installation and usage
+## Installation
 
+Clone repo and build from source:
 ```
-go build -o ./htsget-refserver-utils ./cmd
+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:
 ```
-./htsget-refserver-utils
+go get -u "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
 ```