1e01f41fc6811a3ba9efc853e01a94839f7a91fb braney Thu Mar 31 09:42:58 2011 -0700 add compare routine for cBlocks based on query position diff --git src/inc/chain.h src/inc/chain.h index b7bd9c7..6be0f2a 100644 --- src/inc/chain.h +++ src/inc/chain.h @@ -1,160 +1,163 @@ /* chain - pairwise alignments that can include gaps in both * sequences at once. This is similar in many ways to psl, * but more suitable to cross species genomic comparisons. */ #ifndef CHAIN_H #define CHAIN_H #ifndef LINEFILE_H #include "linefile.h" #endif #ifndef BITS_H #include "bits.h" #endif struct cBlock /* A gapless part of a chain. */ { struct cBlock *next; /* Next in list. */ int tStart,tEnd; /* Range covered in target. */ int qStart,qEnd; /* Range covered in query. */ int score; /* Score of block. */ void *data; /* Some associated data pointer. */ }; +int cBlockCmpQuery(const void *va, const void *vb); +/* Compare to sort based on query start. */ + int cBlockCmpTarget(const void *va, const void *vb); /* Compare to sort based on target start. */ int cBlockCmpBoth(const void *va, const void *vb); /* Compare to sort based on query, then target. */ int cBlockCmpDiagQuery(const void *va, const void *vb); /* Compare to sort based on diagonal, then query. */ void cBlocksAddOffset(struct cBlock *blockList, int qOff, int tOff); /* Add offsets to block list. */ struct cBlock *cBlocksFromAliSym(int symCount, char *qSym, char *tSym, int qPos, int tPos); /* Convert alignment from alignment symbol (bases and dashes) format * to a list of chain blocks. The qPos and tPos correspond to the start * in the query and target sequences of the first letter in qSym and tSym. */ struct chain /* A chain of blocks. Used for output of chainBlocks. */ { struct chain *next; /* Next in list. */ struct cBlock *blockList; /* List of blocks. */ double score; /* Total score for chain. */ char *tName; /* target name, allocated here. */ int tSize; /* Overall size of target. */ /* tStrand always + */ int tStart,tEnd; /* Range covered in target. */ char *qName; /* query name, allocated here. */ int qSize; /* Overall size of query. */ char qStrand; /* Query strand. */ int qStart,qEnd; /* Range covered in query. */ int id; /* ID of chain in file. */ }; void chainFree(struct chain **pChain); /* Free up a chain. */ void chainFreeList(struct chain **pList); /* Free a list of dynamically allocated chain's */ int chainCmpScore(const void *va, const void *vb); /* Compare to sort based on score. */ int chainCmpScoreDesc(const void *va, const void *vb); /* Compare to sort based on score descending. */ int chainCmpTarget(const void *va, const void *vb); /* Compare to sort based on target position. */ int chainCmpQuery(const void *va, const void *vb); /* Compare to sort based on query chrom and start osition. */ void chainWrite(struct chain *chain, FILE *f); /* Write out chain to file in dense format. */ void chainWriteAll(struct chain *chainList, FILE *f); /* Write all chains to file. */ void chainWriteLong(struct chain *chain, FILE *f); /* Write out chain to file in more verbose format. */ void chainWriteHead(struct chain *chain, FILE *f); /* Write chain before block/insert list. */ struct chain *chainRead(struct lineFile *lf); /* Read next chain from file. Return NULL at EOF. * Note that chain block scores are not filled in by * this. */ struct chain *chainReadChainLine(struct lineFile *lf); /* Read line that starts with chain. Allocate memory * and fill in values. However don't read link lines. */ void chainReadBlocks(struct lineFile *lf, struct chain *chain); /* Read in chain blocks from file. */ void chainIdReset(); /* Reset chain id. */ void chainIdNext(struct chain *chain); /* Add id to chain. */ void chainSwap(struct chain *chain); /* Swap target and query side of chain. */ struct hash *chainReadUsedSwap(char *fileName, boolean swapQ, Bits *bits); /* Read chains that are marked as used in the * bits array (which may be NULL) into a hash keyed by id. */ struct hash *chainReadAllSwap(char *fileName, boolean swapQ); /* Read chains into a hash keyed by id. * Set swapQ to True to read chain by query. */ struct hash *chainReadAll(char *fileName); /* Read chains into a hash keyed by id. */ struct hash *chainReadAllWithMeta(char *fileName, FILE *f); /* Read chains into a hash keyed by id and outputs meta data */ struct chain *chainFind(struct hash *hash, int id); /* Find chain in hash, return NULL if not found */ struct chain *chainLookup(struct hash *hash, int id); /* Find chain in hash. */ void chainSubsetOnT(struct chain *chain, int subStart, int subEnd, struct chain **retSubChain, struct chain **retChainToFree); /* Get subchain of chain bounded by subStart-subEnd on * target side. Return result in *retSubChain. In some * cases this may be the original chain, in which case * *retChainToFree is NULL. When done call chainFree on * *retChainToFree. The score and id fields are not really * properly filled in. */ void chainFastSubsetOnT(struct chain *chain, struct cBlock *firstBlock, int subStart, int subEnd, struct chain **retSubChain, struct chain **retChainToFree); /* Get subchain as in chainSubsetOnT. Pass in initial block that may * be known from some index to speed things up. */ void chainSubsetOnQ(struct chain *chain, int subStart, int subEnd, struct chain **retSubChain, struct chain **retChainToFree); /* Get subchain of chain bounded by subStart-subEnd on * query side. Return result in *retSubChain. In some * cases this may be the original chain, in which case * *retChainToFree is NULL. When done call chainFree on * *retChainToFree. The score and id fields are not really * properly filled in. */ void chainRangeQPlusStrand(struct chain *chain, int *retQs, int *retQe); /* Return range of bases covered by chain on q side on the plus * strand. */ #endif /* CHAIN_H */