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Reverted to using a 31-mer for mapping. Lowered MAX_READS.

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jts committed Jun 30, 2012
1 parent 47562c4 commit 30b263f45df8fd3615e2d581dba7ec4c795ddc84
Showing with 6 additions and 4 deletions.
  1. +6 −4 src/GraphDiff/DindelUtil.cpp
@@ -33,15 +33,17 @@ DindelReturnCode DindelUtil::runDindelPairMatePair(const std::string& id,
//
// First, extract the reads from the normal and variant data sets that match each haplotype
//
- size_t MAX_READS = 400000000;
+ assert(inHaplotypes.size() > 0);
+ size_t MAX_READS = 100000;
// Get canidate alignments for the input haplotypes
HapgenAlignmentVector candidateAlignments;
// Choose the kmer size for alignment
- size_t MAX_ALIGN_KMER = 51;
- size_t ALIGN_KMER_OFFSET = 5;
- size_t align_kmer = std::min(MAX_ALIGN_KMER, parameters.kmer - ALIGN_KMER_OFFSET);
+ //size_t MAX_ALIGN_KMER = 51;
+ //size_t ALIGN_KMER_OFFSET = 5;
+ //size_t align_kmer = std::min(MAX_ALIGN_KMER, parameters.kmer - ALIGN_KMER_OFFSET);
+ size_t align_kmer = 31;
for(size_t i = 0; i < inHaplotypes.size(); ++i)
{
HapgenAlignmentVector thisCandidateAlignments;

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