From 40a470762e663c12103de722b844d6a5df65545a Mon Sep 17 00:00:00 2001 From: Michal Kabza Date: Wed, 13 May 2020 00:46:23 +0200 Subject: [PATCH 1/2] Added support for the SPLiTSeq technology --- src/main.cpp | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/src/main.cpp b/src/main.cpp index 0c1e1251..2f9ab73c 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -540,6 +540,7 @@ void ListSingleCellTechnologies() { << "inDropsv3 inDrops version 3 chemistry" << endl << "SCRBSeq SCRB-Seq" << endl << "SureCell SureCell for ddSEQ" << endl + << "SPLiTSeq SPLiTSeq" << endl << endl; } @@ -914,6 +915,12 @@ bool CheckOptionsBus(ProgramOptions& opt) { busopt.seq.push_back(BUSOptionSubstr(1,0,0)); busopt.umi = BUSOptionSubstr(0,0,6); busopt.bc.push_back(BUSOptionSubstr(0,6,16)); + } else if (opt.technology == "SPLITSEQ") { + busopt.seq = BUSOptionSubstr(1,0,0); + busopt.umi = BUSOptionSubstr(0,0,10); + busopt.bc.push_back(BUSOptionSubstr(0,10,18)); + busopt.bc.push_back(BUSOptionSubstr(0,48,56)); + busopt.bc.push_back(BUSOptionSubstr(0,86,94)); } else { vector files; vector values; @@ -1006,6 +1013,13 @@ bool CheckOptionsBus(ProgramOptions& opt) { busopt.umi = BUSOptionSubstr(1,8,14); busopt.bc.push_back(BUSOptionSubstr(0,0,8)); busopt.bc.push_back(BUSOptionSubstr(1,0,8)); + } else if (opt.technology == "SPLITSEQ") { + busopt.nfiles = 2; + busopt.seq = BUSOptionSubstr(1,0,0); + busopt.umi = BUSOptionSubstr(0,0,10); + busopt.bc.push_back(BUSOptionSubstr(0,10,18)); + busopt.bc.push_back(BUSOptionSubstr(0,48,56)); + busopt.bc.push_back(BUSOptionSubstr(0,86,94)); } else { vector files; vector values; From 69b4d9e590d8df107729bbecb50ae3448e4aec34 Mon Sep 17 00:00:00 2001 From: Michal Kabza Date: Tue, 19 May 2020 01:08:19 +0200 Subject: [PATCH 2/2] Updated the SPLiTSeq related code --- src/main.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main.cpp b/src/main.cpp index 2f9ab73c..bc7f1e7a 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -916,7 +916,7 @@ bool CheckOptionsBus(ProgramOptions& opt) { busopt.umi = BUSOptionSubstr(0,0,6); busopt.bc.push_back(BUSOptionSubstr(0,6,16)); } else if (opt.technology == "SPLITSEQ") { - busopt.seq = BUSOptionSubstr(1,0,0); + busopt.seq.push_back(BUSOptionSubstr(1,0,0)); busopt.umi = BUSOptionSubstr(0,0,10); busopt.bc.push_back(BUSOptionSubstr(0,10,18)); busopt.bc.push_back(BUSOptionSubstr(0,48,56)); @@ -1015,7 +1015,7 @@ bool CheckOptionsBus(ProgramOptions& opt) { busopt.bc.push_back(BUSOptionSubstr(1,0,8)); } else if (opt.technology == "SPLITSEQ") { busopt.nfiles = 2; - busopt.seq = BUSOptionSubstr(1,0,0); + busopt.seq.push_back(BUSOptionSubstr(1,0,0)); busopt.umi = BUSOptionSubstr(0,0,10); busopt.bc.push_back(BUSOptionSubstr(0,10,18)); busopt.bc.push_back(BUSOptionSubstr(0,48,56));