Commit 05d961ff authored by Tizian Schulz's avatar Tizian Schulz
Browse files

Removed seed filter

parent acf090f1
......@@ -137,7 +137,7 @@ void extendRefSeeds(ColoredCDBG<seedlist> &cdbg, const string &q, const int16_t
//Filter out some seeds; the second condition ensures that we do not miss seeds in the end of the query.
//Note: What we do not consider here is that some seeds might not be extended to the right because search criteria are not fullfilled anymore. This is intended though. We should not miss too much, because a good hit should have more than one seed
if(newHit.length - currSeed->len > 0 || currSeed->offsetQ + currSeed->len == q.length()){
//if(newHit.length - currSeed->len > 0 || currSeed->offsetQ + currSeed->len == q.length()){
//Extend hit to the left
startLeftX_Drop(&newHit, q, X, quorum, searchSet);
......@@ -154,7 +154,7 @@ void extendRefSeeds(ColoredCDBG<seedlist> &cdbg, const string &q, const int16_t
hitArr[newHit.offQ].nextHit->gAlgn.aSeqG = "";
hitArr[newHit.offQ].nextHit->gAlgn.aSeqQ = "";
}
}
//}
//Delete the extended seed
free(currSeed);
......@@ -198,7 +198,7 @@ void extendRevCompSeeds(ColoredCDBG<seedlist> &cdbg, const string &q, const int1
startRightX_Drop_OnRevComp(&newHit, q, X, quorum, searchSet);
//Filter out some seeds; the second condition ensures that we do not miss seeds in the end of the query and the third that we do not miss seeds in the end of a unitig if the unitig does not have successors (i.e. predecessors on the reference strand)
if(newHit.length - currSeed->len > 0 || currSeed->offsetQ + currSeed->len == q.length() || (!i->getPredecessors().hasPredecessors() && currSeed->offsetU + currSeed->len == i->size)){
//if(newHit.length - currSeed->len > 0 || currSeed->offsetQ + currSeed->len == q.length() || (!i->getPredecessors().hasPredecessors() && currSeed->offsetU + currSeed->len == i->size)){
//Extend hit to the left
startLeftX_Drop_OnRevComp(&newHit, q, X, quorum, searchSet);
......@@ -237,7 +237,7 @@ void extendRevCompSeeds(ColoredCDBG<seedlist> &cdbg, const string &q, const int1
//Copy hit into the array
hitArr[newHit.offQ] = newHit;
}
}
//}
//Delete the extended seed
free(currSeed);
......
CC = g++
CFLAGS = -lbifrost -pthread -lz -lpthread -std=c++11 -Wall -O3
CFLAGS = -lbifrost -pthread -lz -lpthread -std=c++11 -O3
all:
$(CC) PLAST.cpp $(CFLAGS) -o PLAST
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment