blat: inc/chainToPsl.h Source File

00001 /* chainToPsl - convert between chains and psl.  Both of these
00002  * are alignment formats that can handle gaps in both strands
00003  * and do not include the sequence itself. */
00004 
00005 #ifndef CHAINTOPSL_H
00006 #define CHAINTOPSL_H
00007 
00008 #ifndef PSL_H
00009 #include "psl.h"
00010 #endif
00011 
00012 #ifndef CHAINBLOCK_H
00013 #include "chainBlock.h"
00014 #endif
00015 
00016 struct psl *chainToPsl(struct chain *chain);
00017 /* chainToPsl - convert chain to psl.  This does not fill in
00018  * the match, repMatch, mismatch, and N fields since it needs
00019  * the sequence for that.  It does fill in the rest though. */
00020 
00021 struct psl *chainToFullPsl(struct chain *chain, 
00022         struct dnaSeq *query,   /* Forward query sequence. */
00023         struct dnaSeq *rQuery,  /* Reverse complemented query sequence. */
00024         struct dnaSeq *target);
00025 /* Convert chainList to pslList, filling in matches, N's etc. */
00026 
00027 #endif /* CHAINTOPSL_H */
00028