		#!/usr/bin/env node
		var through = require('through2')
		var minimist = require('minimist')
		var bionodeSAM = require('./')

		var args = process.argv.slice(2)
		var args = minimist(process.argv.slice(2))

		var command = args[0] //args.length > 2 ? args.slice(0, args.length-2) : null
		var command = args._[0]
		var lastArg = args._[args._.length - 1]
		var wantsStdin = false
		if (lastArg === '-') {
		wantsStdin = true
		args._.pop()
		}

		var srdDest
		@@ -18,17 +26,15 @@

		process.stdin.setEncoding('utf8');

		if (!process.stdin.isTTY) {
		if (wantsStdin) {
		process.stdin.setEncoding('utf8');

		process.stdin.on('data', function(data) {
		var data = data.trim()
		if (data === '') { return }
		args.push(data.trim())
		var samStream = sam(args)
		args._.push(data.trim())
		var samStream = sam(args._)
		samStream.pipe(JSONstringify()).pipe(process.stdout)
		samStream.on('error', console.log)
		})
		}

		else {
		var samStream = sam(args)
		} else {
		var samStream = sam(args._)
		samStream.pipe(JSONstringify()).pipe(process.stdout)
		@@ -35,0 +41,0 @@ samStream.on('error', console.log)

+3

-2

package.json

		{
		"name": "bionode-sam",
		"description": "Node.js wrapper for samtools.",
		"version": "0.0.5",
		"version": "1.0.1",
		"homepage": "http://github.com/bionode/bionode-sam",
		@@ -15,3 +15,4 @@ "repository": {
		"dependencies": {
		"through2": "~0.5.1"
		"through2": "~0.5.1",
		"minimist": "^1.1.0"
		},
		@@ -18,0 +19,0 @@ "devDependencies": {

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