From d92242b7d9b84395666d55cdc830acfba5de94dd Mon Sep 17 00:00:00 2001 From: Luis Yanes Date: Wed, 7 Aug 2019 15:25:46 +0100 Subject: [PATCH] Closes #18 --- src/modules/w2rap-contigger.cc | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/src/modules/w2rap-contigger.cc b/src/modules/w2rap-contigger.cc index 00d45a8..6c5ffc6 100644 --- a/src/modules/w2rap-contigger.cc +++ b/src/modules/w2rap-contigger.cc @@ -157,7 +157,7 @@ struct cmdline_args { unsigned int from_step=1; unsigned int to_step=8; unsigned int pair_sample=200; - unsigned int disk_batches=0; + unsigned int disk_batches=4; // Enables 4 disk batches by default. Uses less memory on step2 but it is slower unsigned int min_input_reads=3; bool paired_repath=true; bool solve_complex_repeats=false; @@ -627,12 +627,12 @@ int main( int argc, char * argv[]) { OutputLog(2) << "Dumping scaffold_lines..." << std::endl; FinalFiles(hbv, hbvinv, paths, args.out_dir, args.prefix + ".scaffold_lines", MAX_CELL_PATHS, MAX_DEPTH, false); OutputLog(2) << "DONE!" << std::endl; - //TODO: Broken, Luis to FIX -// if (args.output_spectracn){ -// OutputLog(2) << "Computing scaffold_lines freqs..." << std::endl; -// SpectraCN::DumpSpectraCN(args.out_dir+"/"+args.prefix+".scaffold_lines.fasta", args.out_dir,args.prefix+".contig_lines"); -// OutputLog(2) << "DONE!" << std::endl; -// } + + if (args.output_spectracn){ + OutputLog(2) << "Computing scaffold_lines freqs..." << std::endl; + SpectraCN::DumpSpectraCN(args.out_dir+"/"+args.prefix+".scaffold_lines.fasta", args.out_dir,args.prefix+".contig_lines"); + OutputLog(2) << "DONE!" << std::endl; + } } }