87160c4c6abc63ea1732458d5b58ca8bd420528c markd Wed Aug 30 08:53:24 2017 -0700 added option to pslCheck to not check insert sizes diff --git src/inc/psl.h src/inc/psl.h index 5504b31..eac4fb2 100644 --- src/inc/psl.h +++ src/inc/psl.h @@ -1,352 +1,363 @@ /* psl.h was originally generated by the autoSql program, which also * generated psl.c and psl.sql. This header links the database and * the RAM representation of objects. Additional functions were * added later. * * This file is copyright 2002 Jim Kent, but license is hereby * granted for all use - public, private or commercial. */ #ifndef PSL_H #define PSL_H #ifndef LOCALMEM_H #include "localmem.h" #endif #ifndef LINEFILE_H #include "linefile.h" #endif #ifndef FUZZYFIND_H #include "fuzzyFind.h" #endif #ifndef DNASEQ_H #include "dnaseq.h" #endif /* Some forward declarations of structures used but not defined here. */ struct rbTree; #define PSL_NUM_COLS 21 /* number of columns in a PSL */ #define PSLX_NUM_COLS 23 /* number of columns in a PSLX */ #define PSL_XA_FORMAT 0x04 /* add XA format columns */ /* options for pslFromAlign */ #define PSL_IS_SOFTMASK 0x01 /* lower case are mask */ +/* options for pslCheck */ +#define PSL_CHECK_IGNORE_INSERT_CNTS 0x01 /* Don't check insert counts in psl */ + struct psl /* Summary info about a patSpace alignment */ { struct psl *next; /* Next in singly linked list. */ unsigned match; /* Number of bases that match that aren't repeats */ unsigned misMatch; /* Number of bases that don't match */ unsigned repMatch; /* Number of bases that match but are part of repeats */ unsigned nCount; /* Number of 'N' bases */ unsigned qNumInsert; /* Number of inserts in query */ int qBaseInsert; /* Number of bases inserted in query */ unsigned tNumInsert; /* Number of inserts in target */ int tBaseInsert; /* Number of bases inserted in target */ char strand[3]; /* + or - for strand */ char *qName; /* Query sequence name */ unsigned qSize; /* Query sequence size */ int qStart; /* Alignment start position in query */ int qEnd; /* Alignment end position in query */ char *tName; /* Target sequence name */ unsigned tSize; /* Target sequence size */ int tStart; /* Alignment start position in target */ int tEnd; /* Alignment end position in target */ unsigned blockCount; /* Number of blocks in alignment */ unsigned *blockSizes; /* Size of each block */ unsigned *qStarts; /* Start of each block in query. */ unsigned *tStarts; /* Start of each block in target. */ char **qSequence; /* query sequence for each block */ char **tSequence; /* target sequence for each block */ }; struct psl *pslxLoad(char **row); /* Load a pslx from row fetched with select * from psl * from database. Dispose of this with pslFree(). */ struct psl *pslLoad(char **row); /* Load a psl from row fetched with select * from psl * from database. Dispose of this with pslFree(). */ struct psl *pslCommaIn(char **pS, struct psl *ret); /* Create a psl out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new psl */ void pslFree(struct psl **pEl); /* Free a single dynamically allocated psl such as created * with pslLoad(). */ void pslFreeList(struct psl **pList); /* Free a list of dynamically allocated psl's */ void pslOutput(struct psl *el, FILE *f, char sep, char lastSep); /* Print out psl. Separate fields with sep. Follow last field with lastSep. */ #define pslTabOut(el,f) pslOutput(el,f,'\t','\n') /* Print out psl as a line in a tab-separated file. */ #define pslCommaOut(el,f) pslOutput(el,f,',',',') /* Print out psl as a comma separated list including final comma. */ /* ----- end autoSql generated part --------------- */ void pslOutFormat(struct psl *el, FILE *f, char sep, char lastSep); /* Print out selected psl values. Separate fields with sep. Follow last field with lastSep. */ /* Prints out a better format with bold field headings followed by value */ /* Requires further upstream work to ensure that only the field headers */ /* declared here are printed if replacing an existing psl print function*/ struct psl *pslLoadAll(char *fileName); /* Load all psl's in file. */ struct psl *pslNext(struct lineFile *lf); /* Read next line from file and convert it to psl. Return * NULL at eof. */ struct psl *pslxLoadLm(char **row, struct lm *lm); /* Load row into local memory pslx. */ struct psl *pslLoadLm(char **row, struct lm *lm); /* Load row into local memory psl. */ void pslWriteHead(FILE *f); /* Write head of psl. */ void pslxWriteHead(FILE *f, enum gfType qType, enum gfType tType); /* Write head of pslx (extended psl). */ void pslWriteAll(struct psl *pslList, char *fileName, boolean writeHeader); /* Write a psl file from list. */ struct lineFile *pslFileOpen(char *fileName); /* Read header part of psl and make sure it's right. * Return line file handle to it. */ struct lineFile *pslFileOpenWithMeta(char *fileName, FILE *f); /* Read header part of psl and make sure it's right. * Return line file handle to it and send meta data to output file f */ struct lineFile *pslFileOpenWithUniqueMeta(char *fileName, FILE *f); /* Read header part of psl and make sure it's right. * Set flag to suppress duplicate header comments. * Return line file handle to it. */ void pslxFileOpen(char *fileName, enum gfType *retQueryType, enum gfType *retTargetType, struct lineFile **retLf); /* Read header part of psl and make sure it's right. Return * sequence types and file handle. */ void pslxFileOpenWithMeta(char *fileName, enum gfType *retQueryType, enum gfType *retTargetType, struct lineFile **retLf, FILE *f); /* Read header part of psl and make sure it's right. Return * sequence types and file handle and send meta data to output file f */ void pslxFileOpenWithUniqueMeta(char *fileName, enum gfType *retQueryType, enum gfType *retTargetType, struct lineFile **retLf, FILE *f); /* Read header part of psl and make sure it's right. Return * sequence types and file handle and send only unique meta data to output f */ int pslCmpQuery(const void *va, const void *vb); /* Compare to sort based on query. */ int pslCmpTarget(const void *va, const void *vb); /* Compare to sort based on target. */ int pslCmpTargetStart(const void *va, const void *vb); /* Compare to sort based on target start. */ int pslCmpTargetScore(const void *va, const void *vb); /* Compare to sort based on target then score. */ int pslCmpTargetAndStrand(const void *va, const void *vb); /* Compare to sort based on target, strand, tStart. */ int pslCmpScore(const void *va, const void *vb); /* Compare to sort based on score (descending). */ int pslCmpQueryScore(const void *va, const void *vb); /* Compare to sort based on query then score (descending). */ int pslCalcMilliBad(struct psl *psl, boolean isMrna); /* Calculate badness in parts per thousand. */ int pslCmpScoreDesc(const void *va, const void *vb); /* Compare to sort based on score descending. */ int pslCmpMatch(const void *va, const void *vb); /* Compare to sort based on match. */ int pslScore(const struct psl *psl); /* Return score for psl. */ struct ffAli *pslToFfAli(struct psl *psl, struct dnaSeq *query, struct dnaSeq *target, int targetOffset); /* Convert from psl to ffAli format. */ struct ffAli *pslToFakeFfAli(struct psl *psl, DNA *needle, DNA *haystack); /* Convert from psl to ffAli format. In some cases you can pass NULL * for needle and haystack - depending what the post-processing is going * to be. */ struct psl *pslFromFakeFfAli(struct ffAli *ff, DNA *needle, DNA *haystack, char strand, char *qName, int qSize, char *tName, int tSize); /* This will create a basic psl structure from a sorted series of ffAli * blocks. The fields that would need actual sequence to be filled in * are left zero however - fields including match, repMatch, mismatch. */ int pslOrientation(struct psl *psl); /* Translate psl strand + or - to orientation +1 or -1 */ INLINE char pslQStrand(struct psl *psl) /* Get query strand. */ { return psl->strand[0]; } INLINE char pslTStrand(struct psl *psl) /* Get the target strand., Returns implied + when * it's not specific */ { return (psl->strand[1] != '-') ? '+' : '-'; } int pslWeightedIntronOrientation(struct psl *psl, struct dnaSeq *genoSeq, int offset); /* Return >0 if introns make it look like alignment is on + strand, * <0 if introns make it look like alignment is on - strand, * 0 if can't tell. The absolute value of the return indicates * how many splice sites we've seen supporting the orientation. * Sequence should NOT be reverse complemented. */ int pslIntronOrientation(struct psl *psl, struct dnaSeq *genoSeq, int offset); /* Return 1 if introns make it look like alignment is on + strand, * -1 if introns make it look like alignment is on - strand, * 0 if can't tell. * Sequence should NOT be reverse complemented. */ boolean pslHasIntron(struct psl *psl, struct dnaSeq *seq, int seqOffset); /* Return TRUE if there's a probable intron. Sequence should NOT be * reverse complemented. */ void pslTailSizes(struct psl *psl, int *retStartTail, int *retEndTail); /* Find the length of "tails" (rather than extensions) implied by psl. */ void pslRc(struct psl *psl); /* Reverse-complement a PSL alignment. This makes the target strand explicit. */ void pslSwap(struct psl *psl, boolean noRc); /* swap query and target in psl. If noRc is TRUE, don't reverse-complement * PSL if needed, instead make target strand explict. */ void pslTargetOffset(struct psl *psl, int offset); /* Add offset to target positions in psl. */ void pslDump(struct psl *psl, FILE *f); /* Dump most of PSL to file - for debugging. */ struct psl *pslTrimToTargetRange(struct psl *oldPsl, int tMin, int tMax); /* Return psl trimmed to fit inside tMin/tMax. Note this does not * update the match/misMatch and related fields. */ struct psl *pslTrimToQueryRange(struct psl *oldPsl, int qMin, int qMax); /* Return psl trimmed to fit inside qMin/qMax. Note this does not * update the match/misMatch and related fields. */ int pslCheck(char *pslDesc, FILE* out, struct psl* psl); /* Validate a PSL for consistency. pslDesc is printed the error messages * to file out (open /dev/null to discard). Return count of errors. */ +int pslCheck2(unsigned opts, char *pslDesc, FILE* out, struct psl* psl); +/* Validate a PSL for consistency. pslDesc is printed the error messages to + * file out (open /dev/null to discard). Return count of errors. Option + * PSL_CHECK_IGNORE_INSERT_CNTS doesn't validate problems insert counts fields + * in each PSL. Useful because protein PSL doesn't seen to compute these in a + * consistent way. + */ + int pslCountBlocks(struct psl *target, struct psl *query, int maxBlockGap); /* count the number of blocks in the query that overlap the target */ /* merge blocks that are closer than maxBlockGap */ struct hash *readPslToBinKeeper(char *sizeFileName, char *pslFileName); /* read a list of psls and return results in hash of binKeeper structure for fast query*/ boolean pslIsProtein(const struct psl *psl); /* is psl a protein psl (are it's blockSizes and scores in protein space) */ struct psl* pslFromAlign(char *qName, int qSize, int qStart, int qEnd, char *qString, char *tName, int tSize, int tStart, int tEnd, char *tString, char* strand, unsigned options); /* Create a PSL from an alignment. Options PSL_IS_SOFTMASK if lower case * bases indicate repeat masking. Returns NULL if alignment is empty after * triming leading and trailing indels.*/ int pslShowAlignment(struct psl *psl, boolean isProt, char *qName, bioSeq *qSeq, int qStart, int qEnd, char *tName, bioSeq *tSeq, int tStart, int tEnd, FILE *f); /* Show protein/DNA alignment or translated DNA alignment in HTML format. */ int pslGenoShowAlignment(struct psl *psl, boolean isProt, char *qName, bioSeq *qSeq, int qStart, int qEnd, char *tName, bioSeq *tSeq, int tStart, int tEnd, int exnStarts[], int exnEnds[], int exnCnt, FILE *f); /* Show protein/DNA alignment or translated DNA alignment in HTML format. */ struct psl* pslNew(char *qName, unsigned qSize, int qStart, int qEnd, char *tName, unsigned tSize, int tStart, int tEnd, char *strand, unsigned blockSpace, unsigned opts); /* create a new psl with space for the specified number of blocks allocated. * pslGrow maybe used to expand this space if needed. Valid options are * PSL_XA_FORMAT. */ void pslGrow(struct psl *psl, int *blockSpacePtr); /* Increase memory allocated to a psl to hold more blocks. blockSpacePtr * should point the the current maximum number of blocks and will be * updated to with the new amount of space. */ void pslComputeInsertCounts(struct psl *psl); /* compute numInsert and baseInsert fields from the blocks */ struct psl* pslFromGff3Cigar(char *qName, int qSize, int qStart, int qEnd, char *tName, int tSize, int tStart, int tEnd, char* strand, char *cigar); /* create a PSL from a GFF3-style cigar formatted alignment */ int pslRangeTreeOverlap(struct psl *psl, struct rbTree *rangeTree); /* Return amount that psl overlaps (on target side) with rangeTree. */ float pslIdent(struct psl *psl); /* computer fraction identity */ float pslQueryAligned(struct psl *psl); /* compute fraction of query that was aligned */ INLINE unsigned pslQStart(struct psl *psl, int blkIdx) /* return query start for the given block */ { return psl->qStarts[blkIdx]; } INLINE unsigned pslTStart(struct psl *psl, int blkIdx) /* return target start for the given block */ { return psl->tStarts[blkIdx]; } INLINE unsigned pslQEnd(struct psl *psl, int blkIdx) /* return query end for the given block */ { return psl->qStarts[blkIdx] + psl->blockSizes[blkIdx]; } INLINE unsigned pslTEnd(struct psl *psl, int blkIdx) /* return target end for the given block */ { return psl->tStarts[blkIdx] + psl->blockSizes[blkIdx]; } struct psl* pslClone(struct psl *psl); /* clone a psl */ extern char *pslSortList[5]; void pslSortListByVar(struct psl **pslList, char *sort); /* Sort a list of psls using the method definied in the sort string. */ #endif /* PSL_H */