2f48d68cce72bd8ddfb21a11da72d244b7c8c479 markd Sun Oct 3 08:31:41 2010 -0700 added options to specify how to obtained qName and tName. Output query and target defs in score file diff --git src/hg/blastToPsl/pslBuild.h src/hg/blastToPsl/pslBuild.h index b74401a..6481828 100644 --- src/hg/blastToPsl/pslBuild.h +++ src/hg/blastToPsl/pslBuild.h @@ -1,33 +1,36 @@ /* object using in building a PSL from a blast record */ #ifndef pslBuild_h #define pslBuild_h enum /* flags for build, including blast algorithm */ { blastn = 0x001, // blast algorithms blastp = 0x002, blastx = 0x004, tblastn = 0x010, tblastx = 0x020, psiblast = 0x040, bldPslx = 0x080, // construct a PSLx with sequence cnvNucCoords = 0x100, }; -/* score file header */ -extern char *pslBuildScoreHdr; - unsigned pslBuildGetBlastAlgo(char *program); /* determine blast algorithm flags */ struct psl *pslBuildFromHsp(char *qName, int qSize, int qStart, int qEnd, char qStrand, char *qAln, char *tName, int tSize, int tStart, int tEnd, char tStrand, char *tAln, unsigned flags); /* construct a new psl from an HSP. Chaining is left to other programs. */ -void pslBuildWriteScores(FILE* scoreFh, struct psl *psl, double bitScore, double eValue); +FILE *pslBuildScoresOpen(char *scoreFile, bool inclDefs); +/* open score file and write headers */ + +void pslBuildScoresWrite(FILE* scoreFh, struct psl *psl, double bitScore, double eValue); /* write scores for a PSL */ +void pslBuildScoresWriteWithDefs(FILE* scoreFh, struct psl *psl, double bitScore, double eValue, char *qDef, char *tDef); +/* write scores and definitions for a PSL */ + #endif