|
- /* vcmp.h -- reference allele utility functions.
-
- Copyright (C) 2013-2015 Genome Research Ltd.
-
- Author: Petr Danecek <pd3@sanger.ac.uk>
-
- Permission is hereby granted, free of charge, to any person obtaining a copy
- of this software and associated documentation files (the "Software"), to deal
- in the Software without restriction, including without limitation the rights
- to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- copies of the Software, and to permit persons to whom the Software is
- furnished to do so, subject to the following conditions:
-
- The above copyright notice and this permission notice shall be included in
- all copies or substantial portions of the Software.
-
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- THE SOFTWARE. */
-
- #ifndef __VCMP_H__
- #define __VCMP_H__
-
- typedef struct _vcmp_t vcmp_t;
-
- vcmp_t *vcmp_init(void);
- void vcmp_destroy(vcmp_t *vcmp);
-
- /*
- * vcmp_set_ref() - sets and compares reference alleles
- * Returns 0 on success or -1 if alleles not compatible
- */
- int vcmp_set_ref(vcmp_t *vcmp, char *ref1, char *ref2);
-
- /*
- * vcmp_find_allele()
- * @param als1: alternate alleles to ref1 above
- * @param al2: alternate allele to ref2 above
- * Returns -1 if not found or 0-based index to als1 of matching allele
- */
- int vcmp_find_allele(vcmp_t *vcmp, char **als1, int nals1, char *al2);
-
- /*
- * vcmp_map_ARvalues() - Create mapping for Number=A,R tag values
- * @param number: nals2 for Number=R, nals2-1 for Number=A
- * @param nals1: number of alleles
- * @param als1: alleles
- *
- * Returns pointer to an array of size nals2 with mapping from als2
- * to als1 or NULL if REFs (als1[0] and als2[0]) are not compatible.
- * If i is the index of an allele in als2, ret[i] is the index of matching
- * allele in als1 or -1 if als2 does not have a matching allele.
- * The caller must not free the array.
- */
- int *vcmp_map_ARvalues(vcmp_t *vcmp, int number, int nals1, char **als1, int nals2, char **als2);
-
- int *vcmp_map_dipGvalues(vcmp_t *vcmp, int *nmap);
-
- #endif
|
