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#include "Parameters.h"
#include "ErrorWarning.h"
void Parameters::samAttributes(){//everything related to SAM attributes
//outSAMattributes
outSAMattrPresent.NH=false;//TODO re-write as class with constructor?
outSAMattrPresent.HI=false;
outSAMattrPresent.AS=false;
outSAMattrPresent.NM=false;
outSAMattrPresent.MD=false;
outSAMattrPresent.nM=false;
outSAMattrPresent.jM=false;
outSAMattrPresent.jI=false;
outSAMattrPresent.RG=false;
outSAMattrPresent.MC=false;
outSAMattrPresent.XS=false;
outSAMattrPresent.ch=false;
outSAMattrPresent.vA=false;
outSAMattrPresent.vG=false;
outSAMattrPresent.vW=false;
outSAMattrPresent.rB=false;
outSAMattrPresent.ha=false;
outSAMattrPresent.CR=false;
outSAMattrPresent.CY=false;
outSAMattrPresent.UR=false;
outSAMattrPresent.UY=false;
outSAMattrPresent.CB=false;
outSAMattrPresent.UB=false;
outSAMattrPresent.GX=false;
outSAMattrPresent.GN=false;
outSAMattrPresent.sM=false;
outSAMattrPresent.sS=false;
outSAMattrPresent.sQ=false;
outSAMattrPresent.cN=false;
//for quant SAM output only NH and HI flags
outSAMattrPresentQuant=outSAMattrPresent;
outSAMattrPresentQuant.NH=true;
outSAMattrPresentQuant.HI=true;
outSAMattrOrderQuant.push_back(ATTR_NH);
outSAMattrOrderQuant.push_back(ATTR_HI);
vector<string> vAttr1;
if (outSAMattributes.at(0)=="None") {
} else if (outSAMattributes.at(0)=="All"){
vAttr1={"NH","HI","AS","nM","NM","MD","jM","jI","MC","ch"};
} else if (outSAMattributes.at(0)=="Standard"){
vAttr1={"NH","HI","AS","nM"};
} else {
vAttr1=outSAMattributes;
};
for (uint ii=0;ii<vAttr1.size();ii++) {
if (vAttr1.at(ii)== "NH") {
outSAMattrOrder.push_back(ATTR_NH);
outSAMattrPresent.NH=true;
} else if (vAttr1.at(ii)== "HI") {
outSAMattrOrder.push_back(ATTR_HI);
outSAMattrPresent.HI=true;
} else if (vAttr1.at(ii)== "AS") {
outSAMattrOrder.push_back(ATTR_AS);
outSAMattrPresent.AS=true;
} else if (vAttr1.at(ii)== "NM") {
outSAMattrOrder.push_back(ATTR_NM);
outSAMattrPresent.NM=true;
} else if (vAttr1.at(ii)== "MD") {
outSAMattrOrder.push_back(ATTR_MD);
outSAMattrPresent.MD=true;
} else if (vAttr1.at(ii)== "nM") {
outSAMattrOrder.push_back(ATTR_nM);
outSAMattrPresent.nM=true;
} else if (vAttr1.at(ii)== "jM") {
outSAMattrOrder.push_back(ATTR_jM);
outSAMattrPresent.jM=true;
} else if (vAttr1.at(ii)== "jI") {
outSAMattrOrder.push_back(ATTR_jI);
outSAMattrPresent.jI=true;
} else if (vAttr1.at(ii)== "vA") {
outSAMattrOrder.push_back(ATTR_vA);
outSAMattrPresent.vA=true;
} else if (vAttr1.at(ii)== "vG") {
outSAMattrOrder.push_back(ATTR_vG);
outSAMattrPresent.vG=true;
} else if (vAttr1.at(ii)== "vW") {
outSAMattrOrder.push_back(ATTR_vW);
outSAMattrPresent.vW=true;
} else if (vAttr1.at(ii)== "ha") {
outSAMattrOrder.push_back(ATTR_ha);
outSAMattrPresent.ha=true;
} else if (vAttr1.at(ii)== "RG") {
outSAMattrOrder.push_back(ATTR_RG);
outSAMattrOrderQuant.push_back(ATTR_RG);
outSAMattrPresent.RG=true;
} else if (vAttr1.at(ii)== "rB") {
outSAMattrOrder.push_back(ATTR_rB);
outSAMattrOrderQuant.push_back(ATTR_rB);
outSAMattrPresent.rB=true;
} else if (vAttr1.at(ii)== "ch") {
outSAMattrOrder.push_back(ATTR_ch);
outSAMattrOrderQuant.push_back(ATTR_ch);
outSAMattrPresent.ch=true;
} else if (vAttr1.at(ii)== "MC") {
outSAMattrOrder.push_back(ATTR_MC);
outSAMattrOrderQuant.push_back(ATTR_MC);
outSAMattrPresent.MC=true;
} else if (vAttr1.at(ii)== "CR") {
outSAMattrOrder.push_back(ATTR_CR);
outSAMattrOrderQuant.push_back(ATTR_CR);
outSAMattrPresent.CR=true;
} else if (vAttr1.at(ii)== "CY") {
outSAMattrOrder.push_back(ATTR_CY);
outSAMattrOrderQuant.push_back(ATTR_CY);
outSAMattrPresent.CY=true;
} else if (vAttr1.at(ii)== "UR") {
outSAMattrOrder.push_back(ATTR_UR);
outSAMattrOrderQuant.push_back(ATTR_UR);
outSAMattrPresent.UR=true;
} else if (vAttr1.at(ii)== "UY") {
outSAMattrOrder.push_back(ATTR_UY);
outSAMattrOrderQuant.push_back(ATTR_UY);
outSAMattrPresent.UY=true;
} else if (vAttr1.at(ii)== "CB") {
outSAMattrOrder.push_back(ATTR_CB);
outSAMattrOrderQuant.push_back(ATTR_CB);
outSAMattrPresent.CB=true;
} else if (vAttr1.at(ii)== "UB") {
outSAMattrOrder.push_back(ATTR_UB);
outSAMattrOrderQuant.push_back(ATTR_UB);
outSAMattrPresent.UB=true;
} else if (vAttr1.at(ii)== "GX") {
outSAMattrOrder.push_back(ATTR_GX);
outSAMattrOrderQuant.push_back(ATTR_GX);
outSAMattrPresent.GX=true;
} else if (vAttr1.at(ii)== "GN") {
outSAMattrOrder.push_back(ATTR_GN);
outSAMattrOrderQuant.push_back(ATTR_GN);
outSAMattrPresent.GN=true;
} else if (vAttr1.at(ii)== "sM") {
outSAMattrOrder.push_back(ATTR_sM);
outSAMattrOrderQuant.push_back(ATTR_sM);
outSAMattrPresent.sM=true;
} else if (vAttr1.at(ii)== "sS") {
outSAMattrOrder.push_back(ATTR_sS);
outSAMattrOrderQuant.push_back(ATTR_sS);
outSAMattrPresent.sS=true;
} else if (vAttr1.at(ii)== "sQ") {
outSAMattrOrder.push_back(ATTR_sQ);
outSAMattrOrderQuant.push_back(ATTR_sQ);
outSAMattrPresent.sQ=true;
} else if (vAttr1.at(ii)== "cN") {
outSAMattrOrder.push_back(ATTR_cN);
outSAMattrOrderQuant.push_back(ATTR_cN);
outSAMattrPresent.cN=true;
} else if (vAttr1.at(ii)== "XS") {
outSAMattrOrder.push_back(ATTR_XS);
outSAMattrPresent.XS=true;
if (outSAMstrandField.type!=1) {
inOut->logMain << "WARNING --outSAMattributes contains XS, therefore STAR will use --outSAMstrandField intronMotif" <<endl;
outSAMstrandField.type=1;
};
} else {
ostringstream errOut;
errOut <<"EXITING because of FATAL INPUT ERROR: unknown/unimplemented SAM atrribute (tag): "<<vAttr1.at(ii) <<"\n";
errOut <<"SOLUTION: re-run STAR with --outSAMattributes that contains only implemented attributes\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
};
if (!var.yes && (outSAMattrPresent.vA | outSAMattrPresent.vG)) {
ostringstream errOut;
errOut <<"EXITING because of fatal PARAMETER error: --outSAMattributes contains vA and/or vG tag(s), but --varVCFfile is not set\n";
errOut <<"SOLUTION: re-run STAR with a --varVCFfile option, or without vA/vG tags in --outSAMattributes\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
if (!wasp.yes && outSAMattrPresent.vW) {
ostringstream errOut;
errOut <<"EXITING because of fatal PARAMETER error: --outSAMattributes contains vW tag, but --waspOutputMode is not set\n";
errOut <<"SOLUTION: re-run STAR with a --waspOutputMode option, or without vW tags in --outSAMattributes\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
if (outSAMattrRGline[0]!="-" && !outSAMattrPresent.RG) {
outSAMattrOrder.push_back(ATTR_RG);
outSAMattrOrderQuant.push_back(ATTR_RG);
outSAMattrPresent.RG=true;
inOut->logMain << "WARNING --outSAMattrRG defines a read group, therefore STAR will output RG attribute" <<endl;
} else if (outSAMattrRG.size()==0 && outSAMattrPresent.RG) {
ostringstream errOut;
errOut <<"EXITING because of FATAL INPUT ERROR: --outSAMattributes contains RG tag, but --outSAMattrRGline is not set\n";
errOut <<"SOLUTION: re-run STAR with a valid read group parameter --outSAMattrRGline\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
if (outSAMstrandField.type==1 && !outSAMattrPresent.XS) {
outSAMattrOrder.push_back(ATTR_XS);
inOut->logMain << "WARNING --outSAMstrandField=intronMotif, therefore STAR will output XS attribute" <<endl;
};
if (wasp.yes && !outSAMattrPresent.vW) {
outSAMattrOrder.push_back(ATTR_vW);
outSAMattrOrderQuant.push_back(ATTR_vW);
outSAMattrPresent.vW=true;
inOut->logMain << "WARNING --waspOutputMode is set, therefore STAR will output vW attribute" <<endl;
};
//TODO: BAM-only flag should all have values > 100
samAttrRequiresBAM(outSAMattrPresent.ch, "ch");
samAttrRequiresBAM(outSAMattrPresent.CR, "CR");
samAttrRequiresBAM(outSAMattrPresent.CY, "CY");
samAttrRequiresBAM(outSAMattrPresent.UR, "UR");
samAttrRequiresBAM(outSAMattrPresent.UY, "UY");
samAttrRequiresBAM(outSAMattrPresent.CB, "CB");
samAttrRequiresBAM(outSAMattrPresent.UB, "UB");
samAttrRequiresBAM(outSAMattrPresent.sM, "sM");
samAttrRequiresBAM(outSAMattrPresent.sS, "sS");
samAttrRequiresBAM(outSAMattrPresent.sQ, "sQ");
samAttrRequiresBAM(outSAMattrPresent.rB, "rB");
samAttrRequiresBAM(outSAMattrPresent.vG, "vG");
samAttrRequiresBAM(outSAMattrPresent.vA, "vA");
samAttrRequiresBAM(outSAMattrPresent.vW, "vW");
samAttrRequiresBAM(outSAMattrPresent.GX, "GX");
samAttrRequiresBAM(outSAMattrPresent.GN, "GN");
};
void Parameters:: samAttrRequiresBAM(bool attrYes, string attrTag) {
if (!attrYes)
return; // nothing to do
if (!outBAMunsorted && !outBAMcoord) {
ostringstream errOut;
errOut <<"EXITING because of fatal PARAMETER error: --outSAMattributes contains "<< attrTag <<" tag, which requires BAM output.\n";
errOut <<"SOLUTION: re-run STAR with --outSAMtype BAM Unsorted (and/or) SortedByCoordinate option, or without "<< attrTag <<" tag in --outSAMattributes\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
if (outSAMbool)
inOut->logMain << "WARNING: --outSAMattributes contains "<< attrTag <<" tag. It will be output into BAM file(s), but not SAM file.\n";
};
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