1 /*-------------------------------------------------------------------------- 2 * Copyright 2007 utgenome.org 3 * 4 * Licensed under the Apache License, Version 2.0 (the "License"); 5 * you may not use this file except in compliance with the License. 6 * You may obtain a copy of the License at 7 * 8 * http://www.apache.org/licenses/LICENSE-2.0 9 * 10 * Unless required by applicable law or agreed to in writing, software 11 * distributed under the License is distributed on an "AS IS" BASIS, 12 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 * See the License for the specific language governing permissions and 14 * limitations under the License. 15 *--------------------------------------------------------------------------*/ 16 //-------------------------------------- 17 // UTGB Common Project 18 // 19 // PSLPullParser.java 20 // Since: Jun 5, 2007 21 // 22 // $URL$ 23 // $Author$ 24 //-------------------------------------- 25 package org.utgenome.format.psl; 26 27 import java.io.BufferedReader; 28 29 /** 30 * PSL lines represent alignments, and are typically taken from files generated by BLAT or psLayout. See the BLAT documentation for more details. All of the following fields are required on each data 31 * line within a PSL file: 32 * 33 * <pre> 34 * 1. matches - Number of bases that match that aren't repeats 35 * 2. misMatches - Number of bases that don't match 36 * 3. repMatches - Number of bases that match but are part of repeats 37 * 4. nCount - Number of 'N' bases 38 * 5. qNumInsert - Number of inserts in query 39 * 6. qBaseInsert - Number of bases inserted in query 40 * 7. tNumInsert - Number of inserts in target 41 * 8. tBaseInsert - Number of bases inserted in target 42 * 9. strand - '+' or '-' for query strand. In mouse, second '+'or '-' is for genomic strand 43 * 10. qName - Query sequence name 44 * 11. qSize - Query sequence size 45 * 12. qStart - Alignment start position in query 46 * 13. qEnd - Alignment end position in query 47 * 14. tName - Target sequence name 48 * 15. tSize - Target sequence size 49 * 16. tStart - Alignment start position in target 50 * 17. tEnd - Alignment end position in target 51 * 18. blockCount - Number of blocks in the alignment 52 * 19. blockSizes - Comma-separated list of sizes of each block 53 * 20. qStarts - Comma-separated list of starting positions of each block in query 54 * 21. tStarts - Comma-separated list of starting positions of each block in target 55 * </pre> 56 * 57 * @author leo 58 * 59 */ 60 public class PSLPullParser { 61 62 BufferedReader _reader; 63 64 }