This is an automated email from the git hooks/post-receive script. plessy pushed a commit to branch debian/unstable in repository samtools.
commit d09cf942593a00a2fd58d0caa0ad46358639c5c5 Author: Petr Danecek <[email protected]> Date: Fri Dec 6 09:40:13 2013 +0000 Moved khash_utils.h into htslib --- khash_utils.h | 81 ----------------------------------------------------------- stats.c | 2 +- 2 files changed, 1 insertion(+), 82 deletions(-) diff --git a/khash_utils.h b/khash_utils.h deleted file mode 100644 index e277658..0000000 --- a/khash_utils.h +++ /dev/null @@ -1,81 +0,0 @@ -#ifndef __KHASH_UTILS_H__ -#define __KHASH_UTILS_H__ - -#include <htslib/khash.h> - -KHASH_MAP_INIT_STR(str2int, int) - -/* - * Wrappers for khash dictionaries used by mpileup. - */ - -static inline void *khash_str2int_init() -{ - return kh_init(str2int); -} - -/* - * Destroy the hash structure, but not the keys - */ -static inline void khash_str2int_destroy(void *_hash) -{ - khash_t(str2int) *hash = (khash_t(str2int)*)_hash; - if (hash) kh_destroy(str2int, hash); // Note that strings are not freed. -} - -/* - * Destroys both the hash structure and the keys - */ -static inline void khash_str2int_destroy_free(void *_hash) -{ - khash_t(str2int) *hash = (khash_t(str2int)*)_hash; - khint_t k; - if (hash == 0) return; - for (k = 0; k < kh_end(hash); ++k) - if (kh_exist(hash, k)) free((char*)kh_key(hash, k)); - kh_destroy(str2int, hash); -} - -/* - * Returns 1 if key exists or 0 if not - */ -static inline int khash_str2int_has_key(void *_hash, const char *str) -{ - khash_t(str2int) *hash = (khash_t(str2int)*)_hash; - khint_t k = kh_get(str2int, hash, str); - if ( k == kh_end(hash) ) return 0; - return 1; -} - -/* - * Returns 0 on success and -1 when the key is not present. On success, - * *value is set, unless NULL is passed. - */ -static inline int khash_str2int_get(void *_hash, const char *str, int *value) -{ - khash_t(str2int) *hash = (khash_t(str2int)*)_hash; - khint_t k; - if ( !hash ) return -1; - k = kh_get(str2int, hash, str); - if ( k == kh_end(hash) ) return -1; - if ( !*value ) return 0; - *value = kh_val(hash, k); - return 0; -} - -/* - * Add a new string to the dictionary, auto-incrementing the value. - */ -static inline int khash_str2int_inc(void *_hash, const char *str) -{ - khint_t k; - int ret; - khash_t(str2int) *hash = (khash_t(str2int)*)_hash; - if ( !hash ) return -1; - k = kh_put(str2int, hash, str, &ret); - if (ret == 0) return kh_val(hash, k); - kh_val(hash, k) = kh_size(hash) - 1; - return kh_val(hash, k); -} - -#endif diff --git a/stats.c b/stats.c index 45864d9..3c1e78e 100644 --- a/stats.c +++ b/stats.c @@ -27,7 +27,7 @@ #include <htslib/faidx.h> #include "sam.h" // have to keep local version because of sam header parsing. todo: migrate to htslib #include "sam_header.h" // -#include "khash_utils.h" +#include <htslib/khash_str2int.h> #include "samtools.h" #define BWA_MIN_RDLEN 35 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/samtools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
