Skip to content

Allow vW:i tag for wasp in SAM output #2617

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
ASLeonard wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Allow vW:i tag for wasp in SAM output #2617

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 0 additions & 7 deletions source/Parameters.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -880,13 +880,6 @@ void Parameters::inputParameters (int argInN, char* argIn[]) {//input parameters
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};

if (wasp.yes && outSAMtype.at(0)!="BAM") {
ostringstream errOut;
errOut <<"EXITING because of FATAL INPUT ERROR: --waspOutputMode requires output to BAM file\n";
errOut <<"SOLUTION: re-run STAR with --waspOutputMode ... and --outSAMtype BAM ... \n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};

//quantification parameters
quant.yes=false;
quant.geCount.yes=false;
Expand Down
3 changes: 1 addition & 2 deletions source/Parameters_samAttributes.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -237,7 +237,6 @@ void Parameters::samAttributes(){//everything related to SAM attributes
samAttrRequiresBAM(outSAMattrPresent.rB, "rB");
samAttrRequiresBAM(outSAMattrPresent.vG, "vG");
samAttrRequiresBAM(outSAMattrPresent.vA, "vA");
samAttrRequiresBAM(outSAMattrPresent.vW, "vW");
samAttrRequiresBAM(outSAMattrPresent.GX, "GX");
samAttrRequiresBAM(outSAMattrPresent.GN, "GN");

Expand All @@ -260,4 +259,4 @@ void Parameters:: samAttrRequiresBAM(bool attrYes, string attrTag) {

if (outSAMbool)
inOut->logMain << "WARNING: --outSAMattributes contains "<< attrTag <<" tag. It will be output into BAM file(s), but not SAM file.\n";
};
};
3 changes: 3 additions & 0 deletions source/ReadAlign_outputTranscriptSAM.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -337,6 +337,9 @@ uint ReadAlign::outputTranscriptSAM(Transcript const &trOut, uint nTrOut, uint i
case ATTR_vG:
case ATTR_vA:
case ATTR_vW:
if (waspType!=-1)
*outStream<< "\tvW:i:" << (int32)waspType;
break;
case ATTR_GX:
case ATTR_GN:
break;
Expand Down