From 84a877bbc166a5f417d2ac840da261f5d4515a0c Mon Sep 17 00:00:00 2001
From: Veronique Legrand <vlegrand@pasteur.fr>
Date: Tue, 15 Mar 2016 13:56:19 +0100
Subject: [PATCH] bug fix+ traces for debug
---
src/rock.cpp | 30 +++++++++++++++++++-----------
1 file changed, 19 insertions(+), 11 deletions(-)
diff --git a/src/rock.cpp b/src/rock.cpp
index 24391ec..c915439 100644
--- a/src/rock.cpp
+++ b/src/rock.cpp
@@ -30,6 +30,7 @@
using namespace std;
+//#define DEBUG
#define BENCHMARK
#ifdef BENCHMARK
@@ -121,24 +122,31 @@ void lowFilterCMS(FqBaseBackend* map_id_backend[],int nb_be,int k, CountMinSketc
for (i=0;i<nb_be;i++){
map_id_backend[i]->openFile();
}
-
+ cout<<"all input files are open"<<endl;
for (it=io_sr->begin(); it!=io_sr->end(); ++it) {
for (it_offs=it->second.begin();it_offs!=it->second.end();it_offs++) {
unsigned int j=it_offs->first;
for (it_struct=it_offs->second.begin();it_struct!=it_offs->second.end();it_struct++) {
- // read dna string corresponding to fastq record
- DnaSeqStr a_seqs[2];
- init_DnaSeqStr(&a_seqs[0]);
- init_DnaSeqStr(&a_seqs[1]);
- getDNASeqstr(map_id_backend,*it_struct,j,a_seqs);
- // decompose dna string into k-mers and turn k_mers into numbers.
- decomposeReadInKMerNums(read_p, nbrKmerDecompo,k,a_seqs);
- ret=pcms->isBeneathMinKappa(nbrKmerDecompo);
- if (ret) it_struct->fileid=0;
- nbrKmerDecompo.clear();
+ if (it_struct->fileid) {
+ // read dna string corresponding to fastq record
+ DnaSeqStr a_seqs[2];
+ init_DnaSeqStr(&a_seqs[0]);
+ init_DnaSeqStr(&a_seqs[1]);
+ getDNASeqstr(map_id_backend,*it_struct,j,a_seqs);
+#ifdef DEBUG
+cout<<a_seqs[0].fq_record_buf<<" "<<a_seqs[0].start_idx<<" "<<a_seqs[0].length<<endl;
+cout<<a_seqs[1].fq_record_buf<<" "<<a_seqs[1].start_idx<<" "<<a_seqs[1].length<<endl;
+#endif
+ // decompose dna string into k-mers and turn k_mers into numbers.
+ decomposeReadInKMerNums(read_p, nbrKmerDecompo,k,a_seqs);
+ ret=pcms->isBeneathMinKappa(nbrKmerDecompo);
+ if (ret) it_struct->fileid=0;
+ nbrKmerDecompo.clear();
+ }
}
}
}
+ cout<<"going to close input files."<<endl;
for (i=0;i<nb_be;i++){
map_id_backend[i]->closeFile();
}
--
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