SAM format parser, with the hability to retrive regions from a ws
Install the module with: npm install biojs-io-sam
var biojsiosam = require('biojs-io-sam');
biojsiosam.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.
Please submit all issues and pull requests to the homonecloco/biojs-io-sam repository!
If you have any problem or suggestion please open an issue here.
Write the documentation of all the methods to query the flags and so on.
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.