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with full coverage statistic

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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/branches/eric-test@188 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
Eric Coissac
2009-03-15 21:52:29 +00:00
parent 9908a40aaa
commit 5d212d5753
1 changed files with 15 additions and 4 deletions
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19
src/libecoprimer/ecoprimer.h
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@ -157,6 +157,8 @@ typedef struct {
uint32_t inexample; //< example sequence count
uint32_t outexample; //< counterexample sequence count
uint32_t intaxa; //< example taxa count
uint32_t outtaxa; //< counterexample taxa count
@ -169,10 +171,6 @@ typedef struct {
float quorumin;
float quorumout;
//
// uint32_t ampsetcount;
// uint32_t ampsetindex;
// pampseqset_t ampset;
//
// uint32_t taxsetcount;
// uint32_t taxsetindex;
// ptaxampset_t taxset;
@ -237,9 +235,14 @@ typedef struct {
bool_t no_multi_match;
char taxonrank[20]; //TR to count ranks against a pair
int32_t taxonrankidx; //TR to count ranks against a pair
// Some statistics useful for options filters
int32_t dbsize;
int32_t insamples;
int32_t outsamples;
int32_t intaxa;
int32_t outtaxa;
} options_t, *poptions_t;
typedef ecoseq_t **pecodnadb_t;
@ -291,4 +294,12 @@ ppair_t insertpair(pair_t key,ppairtree_t list);
/*TR: Added*/
ppairtree_t buildPrimerPairs(pecodnadb_t seqdb,uint32_t seqdbsize,pprimercount_t primers,poptions_t options);
int32_t counttaxon(int32_t taxid);
int32_t getrankdbstats(pecodnadb_t seqdb,
uint32_t seqdbsize,
ecotaxonomy_t *taxonomy,
poptions_t options);
float taxonomycoverage(ppair_t pair, poptions_t options);
#endif /* EPSORT_H_ */