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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@216 60f365c0-8329-0410-b2a4-ec073aeeaa1d

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This commit is contained in:
Eric Coissac
2009-05-13 09:26:57 +00:00
parent c192908469
commit 40644bc85f
2 changed files with 6 additions and 8 deletions
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src/ecoPrimer
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src/libecoprimer/filtering.c
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@ -117,7 +117,6 @@ static int32_t *ecoFilteringHashSequence(int32_t *dest,
code = encoder[(*base) - 'A']; code = encoder[(*base) - 'A'];
if (code <0) if (code <0)
{ {
//DEBUG_LOG("Error on seq %s @ %d --> %c",seq->AC,j,*base);
code = 0; code = 0;
error|= 1; error|= 1;
} }
@ -128,11 +127,12 @@ static int32_t *ecoFilteringHashSequence(int32_t *dest,
if (!error) if (!error)
{ {
// DEBUG_LOG("No Error on %s @ %d",seq->AC,j); if (doublestrand)
goodword=(uint32_t)((doublestrand) ? MINI(word,antiword):word); goodword=(uint32_t)MINI(word,antiword);
else
goodword=word;
if (!in_last_seq[goodword]) if (!in_last_seq[goodword])
{ {
// DEBUG_LOG("Store word %s",ecoUnhashWord(goodword,FWORDSIZE))
in_last_seq[goodword]=1; in_last_seq[goodword]=1;
dest[goodword]++; dest[goodword]++;
} }
@ -172,17 +172,15 @@ int32_t *filteringSeq(pecodnadb_t database, uint32_t seqdbsize,
for (i=0;i<*size;i++) for (i=0;i<*size;i++)
if (wordscount[i] >= sequenceQuorum) if (wordscount[i] >= sequenceQuorum)
keep++; keep++;
// else if (wordscount[i])
// DEBUG_LOG("Word : %s -> %d",ecoUnhashWord(i,FWORDSIZE),wordscount[i]);
(void)ecoFilteringHashSequence((int32_t*)-1, (void)ecoFilteringHashSequence((int32_t*)-1,
options->circular, options->circular,
options->doublestrand, options->doublestrand,
NULL, NULL,
NULL); NULL);
fprintf(stderr,"ok\n Considered word of size %d for filtering with quorum >= %d : %d\n",FWORDSIZE,sequenceQuorum,keep); fprintf(stderr,"ok\n Considered word of size %d for filtering : %d\n",FWORDSIZE,keep);
return wordscount; return wordscount;
} }