From 1e1af1a6d6afd97ec1f0339cdea92a8a5bcbebf2 Mon Sep 17 00:00:00 2001
From: ASLeonard <tkom343@gmail.com>
Date: Fri, 11 Apr 2025 14:16:53 +0200
Subject: [PATCH] allow vW for wasp in SAM output

---
 source/Parameters.cpp                    | 7 -------
 source/Parameters_samAttributes.cpp      | 3 +--
 source/ReadAlign_outputTranscriptSAM.cpp | 3 +++
 3 files changed, 4 insertions(+), 9 deletions(-)

diff --git a/source/Parameters.cpp b/source/Parameters.cpp
index 26f6a2dd..ce25c616 100755
--- a/source/Parameters.cpp
+++ b/source/Parameters.cpp
@@ -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;
diff --git a/source/Parameters_samAttributes.cpp b/source/Parameters_samAttributes.cpp
index 9508496f..d5b3941a 100644
--- a/source/Parameters_samAttributes.cpp
+++ b/source/Parameters_samAttributes.cpp
@@ -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");
     
@@ -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";
-};
\ No newline at end of file
+};
diff --git a/source/ReadAlign_outputTranscriptSAM.cpp b/source/ReadAlign_outputTranscriptSAM.cpp
index c947e1a0..80078f24 100755
--- a/source/ReadAlign_outputTranscriptSAM.cpp
+++ b/source/ReadAlign_outputTranscriptSAM.cpp
@@ -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;