biojs-io-sam

SAM format parser, with the hability to retrive regions from a ws

Getting Started

Install the module with: npm install biojs-io-sam

var biojsiosam = require('biojs-io-sam');
biojsiosam.parseSam(stringWithSamFile); 

Documentation

.parseSam(stringWithSamFile)

Parameter: stringWithSamFile Type: String Example:

test\_1	0	chr\_2	225	1	70M	*	0	0	TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:70	YT:Z:UU
test\_2	0	chr\_2	73	1	70M	*	0	0	CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:70	YT:Z:UU

This methods returns an array of string lines, wach one with the properties.

Contributing

Please submit all issues and pull requests to the homonecloco/biojs-io-sam repository!

Support

If you have any problem or suggestion please open an issue here.

TODO

Write the documentation of all the methods to query the flags and so on.

License

This software is licensed under the Apache 2 license, quoted below.

Copyright (c) 2014, Ricardo H. Ramirez-Gonzalez

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.