modifying kraken output to include dna seq

agarg2008 · Nov 6, 2015 · 060af46 · 060af46
1 parent 93f2cd7
commit 060af46
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/scripts/build_kraken_db.sh b/scripts/build_kraken_db.sh
@@ -72,7 +72,7 @@ else
   # Estimate hash size as 1.15 * chars in library FASTA files
   if [ -z "$KRAKEN_HASH_SIZE" ]
   then
-    KRAKEN_HASH_SIZE=$(find library/ '(' -name '*.fna' -o -name '*.fa' -o -name '*.ffn' ')' -printf '%s\n' | perl -nle '$sum += $_; END {print int(1.15 * $sum)}')
+    KRAKEN_HASH_SIZE=$(gfind library/ '(' -name '*.fna' -o -name '*.fa' -o -name '*.ffn' ')' -printf '%s\n' | perl -nle '$sum += $_; END {print int(1.15 * $sum)}')
     echo "Hash size not specified, using '$KRAKEN_HASH_SIZE'"
   fi
 

diff --git a/src/Makefile b/src/Makefile
@@ -1,4 +1,4 @@
-CXX = g++
+CXX = g++-5
 CXXFLAGS = -Wall -fopenmp -O3
 PROGS = db_sort set_lcas classify make_seqid_to_taxid_map db_shrink
 

diff --git a/src/classify.cpp b/src/classify.cpp
@@ -278,7 +278,7 @@ void classify_sequence(DNASequence &dna, ostringstream &koss,
       return;
     koss << "U\t";
   }
-  koss << dna.id << "\t" << call << "\t" << dna.seq.size() << "\t";
+  koss << dna.id << "\t" << call << "\t" << dna.seq.size() << "\t" << dna.seq << "\t";
 
   if (Quick_mode) {
     koss << "Q:" << hits;