From cb9b7b7ec63ae5890bbcfab2a7e6c0eaa7ce605d Mon Sep 17 00:00:00 2001 From: Feng Yan Date: Mon, 20 Jul 2020 15:28:26 +1000 Subject: [PATCH 1/2] Update alignToMeth.cpp fix error on reading patterns on the reverse strand. The XM tag is coded based on CG content on reverse strand, but the order of the string is based on 5' to 3', see issue #4 --- src/alignToMeth.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/alignToMeth.cpp b/src/alignToMeth.cpp index 94d0bc1..16770aa 100644 --- a/src/alignToMeth.cpp +++ b/src/alignToMeth.cpp @@ -27,7 +27,7 @@ int byread(BamTools::BamAlignment al, al.GetTag("XM:Z:", Meth); std::string strand="+"; if (al.IsReverseStrand()) { - std::reverse(Meth.begin(), Meth.end()); + // std::reverse(Meth.begin(), Meth.end()); strand="-"; } for (int i = 0; i < al.QueryBases.size(); i++) { From c1eafbaba7a8567ace1ee3724cd60a8dd7ce8abc Mon Sep 17 00:00:00 2001 From: Feng Yan Date: Fri, 11 Sep 2020 14:11:34 +1000 Subject: [PATCH 2/2] Update main.cpp change the coverage cutoff to 10. Need more processing time compare to 60x, but can be subjected to different cutoff later. --- src/main.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main.cpp b/src/main.cpp index 741f06c..44d0084 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -25,7 +25,7 @@ int main(int argc, const char * argv[]) //default distance cutoff: 72 // trying to match seq length int d=72; //default read coverage: 60 - int cov=60; + int cov=10; std::cerr << "Default program paramters for methclone: \nMax loci width: " << d << " bp" << std::endl; std::cerr << "Min methylation difference cutoff: " << m << "%" << std::endl;