v11.6 - GCnorm

Author: valeu

src/GenomeCopyNumber.cpp

@@ -2388,9 +2388,6 @@ void GenomeCopyNumber::calculateCopyNumberProbs_and_genomeLength(int breakPointT
                 realEndOfTheCNV=it->getChrLength();
 
             if (sex_.compare("XY")==0 && (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) {
-                if ((cnumber != normalXYploidy)&&(cnumber != NA))
-                    CNVs_.push_back(EntryCNV(it->getChromosome(),start,end,start*windowSize_,realEndOfTheCNV,cnumber)); //save previous CNV
-
                 if ((cnumber != normalXYploidy)&&(cnumber != NA))
                     if (hasBAF_)
                         CNVs_.push_back(EntryCNV(it->getChromosome(),start,end,start*windowSize_,realEndOfTheCNV,cnumber,lUncertainty, lBAF,hasBAF_)); //save previous CNV

src/Makefile.freec

@@ -12,7 +12,14 @@ EXTRA_CXXFLAGS = -DPROFILE_TRACE
 
 EXTRA_LDFLAGS = -lpthread
 
-CXXFLAGS = $(CXXOPT) $(EXTRA_CXXFLAGS) -Wall -m64
+M64_FLAG := -m64
+ifeq (aarch64,$(shell uname -m))
+        M64_FLAG =
+endif
+
+
+
+CXXFLAGS = $(CXXOPT) $(EXTRA_CXXFLAGS) -Wall $(M64_FLAG)
 
 MAKEDEPEND = gcc -M $(EXTRA_CXXFLAGS)
 
@@ -21,7 +28,7 @@ PROG = freec
 all: $(PROG)
 
 $(PROG): main.o ConfigFile.o Chameleon.o GenomeDensity.o Help.o myFunc.o KernelVector.o ChrDensity.o ChrCopyNumber.o GenomeCopyNumber.o chisquaredistr.o ap.o igammaf.o gammafunc.o normaldistr.o ablasf.o ablas.o ortfac.o sblas.o rotations.o reflections.o linreg.o hblas.o descriptivestatistics.o creflections.o blas.o bdsvd.o svd.o ialglib.o EntryCNV.o SNPinGenome.o SNPatChr.o SNPposition.o binomialdistr.o ibetaf.o ThreadPool.o BAFpileup.o SeekSubclones.o
-	 g++ -m64 $(CXXOPT) -o $(PROG) $+ $(EXTRA_LDFLAGS)
+	 g++ $(M64_FLAG) $(CXXOPT) -o $(PROG) $+ $(EXTRA_LDFLAGS)
 
 init: