00001 /***************************************************************************** 00002 * Copyright (C) 2000 Jim Kent. This source code may be freely used * 00003 * for personal, academic, and non-profit purposes. Commercial use * 00004 * permitted only by explicit agreement with Jim Kent (jim_kent@pacbell.net) * 00005 *****************************************************************************/ 00006 /* crudeAli.h - Interface to the fast, crude blast-like aligner. */ 00007 00008 #ifndef CRUDEALI_H 00009 #define CRUDEALI_H 00010 00011 struct crudeAli 00012 /* Stored info on a crude alignment. */ 00013 { 00014 struct crudeAli *next; 00015 int chromIx; 00016 int start, end; 00017 int score; 00018 char strand; 00019 int qStart, qEnd; 00020 }; 00021 00022 struct crudeAli *crudeAliFind(DNA *probe, int probeSize, struct nt4Seq **chrome, int chromeCount, int tileSize, int minScore); 00023 /* Returns a list of crude alignments. (You can free this with slFreeList() */ 00024 00025 #endif /* CRUDEALI_H */ 00026
1.5.2