obitools/ecoprimers
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 2 Wiki Activity

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@215 60f365c0-8329-0410-b2a4-ec073aeeaa1d

Browse Source
This commit is contained in:
Eric Coissac
2009-05-13 09:18:24 +00:00
parent b0521a7e15
commit c192908469
1 changed files with 7 additions and 2 deletions
Download Patch File Download Diff File Expand all files Collapse all files

9
src/libecoprimer/filtering.c
View File

@ -117,6 +117,7 @@ static int32_t *ecoFilteringHashSequence(int32_t *dest,
code = encoder[(*base) - 'A'];
if (code <0)
{
//DEBUG_LOG("Error on seq %s @ %d --> %c",seq->AC,j,*base);
code = 0;
error|= 1;
}
@ -127,9 +128,11 @@ static int32_t *ecoFilteringHashSequence(int32_t *dest,
if (!error)
{
// DEBUG_LOG("No Error on %s @ %d",seq->AC,j);
goodword=(uint32_t)((doublestrand) ? MINI(word,antiword):word);
if (!in_last_seq[goodword])
{
// DEBUG_LOG("Store word %s",ecoUnhashWord(goodword,FWORDSIZE))
in_last_seq[goodword]=1;
dest[goodword]++;
}
@ -169,15 +172,17 @@ int32_t *filteringSeq(pecodnadb_t database, uint32_t seqdbsize,
for (i=0;i<*size;i++)
if (wordscount[i] >= sequenceQuorum)
keep++;
// else if (wordscount[i])
// DEBUG_LOG("Word : %s -> %d",ecoUnhashWord(i,FWORDSIZE),wordscount[i]);
(void)ecoFilteringHashSequence((int32_t*)-1,
options->circular,
options->circular,
options->doublestrand,
NULL,
NULL);
fprintf(stderr,"ok\n Considered word of size %d for filtering : %d\n",FWORDSIZE,keep);
fprintf(stderr,"ok\n Considered word of size %d for filtering with quorum >= %d : %d\n",FWORDSIZE,sequenceQuorum,keep);
return wordscount;
}