bionode-sam - npm Package Compare versions

Comparing version 0.0.3 to 0.0.4

cli.js

		@@ -10,3 +10,2 @@ #!/usr/bin/env node

		console.log(command)
		// if (args.length === 0) { throw Error('Please specify command and files') }
		@@ -20,10 +19,30 @@ // else if (args.length === 1) { throw Error('Please provide a SRA file') }

		var samStream = sam(args)
		process.stdin.setEncoding('utf8');

		samStream.on('data', function(data) {
		process.stdout.write(data[0]+' -> '+data[1]+'\n')
		})
		if (!process.stdin.isTTY) {
		process.stdin.on('data', function(data) {
		var data = data.trim()
		if (data === '') { return }
		args.push(data.trim())
		var samStream = sam(args)
		samStream.pipe(JSONstringify()).pipe(process.stdout)
		samStream.on('error', console.log)
		})
		}

		samStream.on('error', function(error) {
		console.error(error)
		})
		else {
		var samStream = sam(args)
		samStream.pipe(JSONstringify()).pipe(process.stdout)
		samStream.on('error', console.log)
		}

		function JSONstringify() {
		var stream = through.obj(transform)
		return stream
		function transform(obj, enc, next) {
		try { obj = JSON.stringify(obj) }
		catch(e) {}
		if (obj !== '') { this.push(obj + '\n') }
		next()
		}
		}

lib/bionode-sam.js

		@@ -37,6 +37,6 @@ var path = require('path')

		if (Arg1Ext === 'sam' && Arg2Ext === 'bam') {
		if (Arg1Ext === 'sam') {
		// sam to bam conversion
		// samtools view -bS -o aln.bam aln.sam
		console.log('sam -> bam')
		obj[1] = obj[1] \|\| obj[0].replace('.sam', '.bam')
		multi = true
		@@ -58,2 +58,8 @@ var samToBam = spawn(samPath, [ 'view', '-bS', '-o', obj[1].replace('.bam', '.unsorted.bam'), obj[0] ])
		else {
		var output = {
		sam: obj[0],
		bam: obj[1],
		operation: "sam -> bam"
		}
		self.push(output)
		next()
		@@ -102,3 +108,3 @@ }

		else if (obj[0].indexOf('.fa') !== -1 && Arg2Ext === 'bam' && Arg3Ext === 'bcf') {
		else if (obj[0].indexOf('.fna') !== -1 && Arg2Ext === 'bam' && Arg3Ext === 'bcf') {
		// bam to bcf conversion with reference
		@@ -105,0 +111,0 @@ // samtools mpileup -C50 -uf ref.fa aln.bam > aln.bcf

package.json

		{
		"name": "bionode-sam",
		"description": "Node.js wrapper for samtools.",
		"version": "0.0.3",
		"version": "0.0.4",
		"homepage": "http://github.com/bionode/bionode-sam",
		@@ -6,0 +6,0 @@ "repository": {

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