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more documentation in ksw.h

This commit is contained in:
Heng Li 2013-02-27 21:40:46 -05:00
parent 4bb0bdddca
commit 64d92d26df
2 changed files with 51 additions and 11 deletions
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17
Makefile
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@ -28,14 +28,19 @@ bwa:libbwa.a $(AOBJS) main.o
libbwa.a:$(LOBJS)
$(AR) -csru $@ $(LOBJS)
QSufSort.o:QSufSort.h
bwt_gen.o:QSufSort.h
ksw.o:ksw.h
kstring.o:kstring.h
utils.o:utils.h ksort.h kseq.h
bntseq.o:bntseq.h
bwt.o:bwt.h utils.h
bwa.o:bwa.h
bwa.o:bwa.h bwt.h bntseq.h
bwamem.o:ksw.h kbtree.h ksort.h kvec.h kstring.h utils.h bwamem.h
bwamem_pair.o:ksw.h kvec.h kstring.h utils.h bwamem.h
QSufSort.o:QSufSort.h
bwt_gen.o:QSufSort.h
fastmap.o:bwt.h bwamem.h
bwtaln.o:bwt.h bwtaln.h kseq.h
bwtgap.o:bwtgap.h bwtaln.h bwt.h
@ -44,9 +49,5 @@ bwtsw2_core.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
bwtsw2_aux.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
bwtsw2_main.o:bwtsw2.h
bwamem.o:bwamem.h
bwamem_pair.o:bwamem.h
fastmap.o:bwt.h bwamem.h
clean:
rm -f gmon.out *.o a.out $(PROG) *~ *.a

45
ksw.h
View File

@ -30,7 +30,7 @@ extern "C" {
* @param tlen length of the target sequence
* @param target target sequence
* @param m number of residue types
* @param mat m*m scoring matrix in one-dimention array
* @param mat m*m scoring matrix in one-dimension array
* @param gapo gap open penalty; a gap of length l cost "-(gapo+l*gape)"
* @param gape gap extension penalty
* @param xtra extra information (see below)
@ -62,8 +62,47 @@ extern "C" {
*/
kswr_t ksw_align(int qlen, uint8_t *query, int tlen, uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int xtra, kswq_t **qry);
int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int h0, int *_qle, int *_tle, int *_gtle, int *_gscore);
int ksw_global(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int *_n_cigar, uint32_t **_cigar);
/**
* Banded global alignment
*
* @param qlen query length
* @param query query sequence with 0 <= query[i] < m
* @param tlen target length
* @param target target sequence with 0 <= target[i] < m
* @param m number of residue types
* @param mat m*m scoring mattrix in one-dimension array
* @param gapo gap open penalty; a gap of length l cost "-(gapo+l*gape)"
* @param gape gap extension penalty
* @param w band width
* @param n_cigar (out) number of CIGAR elements
* @param cigar (out) BAM-encoded CIGAR; caller need to deallocate with free()
*
* @return score of the alignment
*/
int ksw_global(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int *n_cigar, uint32_t **cigar);
/**
* Extend alignment
*
* The routine aligns $query and $target, assuming their upstream sequences,
* which are not provided, have been aligned with score $h0. In return,
* region [0,*qle) on the query and [0,*tle) on the target sequences are
* aligned together. If *gscore>=0, *gscore keeps the best score such that
* the entire query sequence is aligned; *gtle keeps the position on the
* target where *gscore is achieved. Returning *gscore and *gtle helps the
* caller to decide whether an end-to-end hit or a partial hit is preferred.
*
* The first 9 parameters are identical to those in ksw_global()
*
* @param h0 alignment score of upstream sequences
* @param _qle (out) length of the query in the alignment
* @param _tle (out) length of the target in the alignment
* @param _gtle (out) length of the target if query is fully aligned
* @param _gscore (out) score of the best end-to-end alignment; negative if not found
*
* @return best semi-local alignment score
*/
int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int h0, int *qle, int *tle, int *gtle, int *gscore);
#ifdef __cplusplus
}