From d73b94b961ad84388fe6ad83ad22dda7b3ec4aca Mon Sep 17 00:00:00 2001 From: Jeremiah Wala Date: Thu, 18 Jun 2015 17:00:15 -0400 Subject: [PATCH] fixed region error --- src/variant.cpp | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/src/variant.cpp b/src/variant.cpp index 9b3524a..ac75961 100644 --- a/src/variant.cpp +++ b/src/variant.cpp @@ -137,13 +137,12 @@ int main(int argc, char** argv) { if (opt::verbose) std::cerr << "...rules: " << opt::rules << std::endl; walk.SetMiniRulesCollection(opt::rules); - + // set the regions to run if (grv_proc_regions.size()) walk.setBamWalkerRegions(grv_proc_regions.asGenomicRegionVector()); - - /*SnowTools::GRC rules_rg = walk.GetMiniRulesCollection().getAllRegions(); + SnowTools::GRC rules_rg = walk.GetMiniRulesCollection().getAllRegions(); rules_rg.createTreeMap(); if (grv_proc_regions.size() && rules_rg.size()) // intersect rules regions with mask regions @@ -156,7 +155,7 @@ int main(int argc, char** argv) { } else if (!rules_rg.size() && grv_proc_regions.size() > 0) { std::cerr << "No regions with possibility of reads. This error occurs if no regions in -g are in -k." << std::endl; return 1; - }*/ + } // should we count all rules (slower) if (opt::counts_only || opt::counts_file.length())