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STAR-2.7.10a/source/htslib/knetfile.c STAR-2.7.10a/source/htslib/kstring.c STAR-2.7.10a/source/htslib/sam.5 STAR-2.7.10a/source/htslib/sam.c STAR-2.7.10a/source/htslib/synced_bcf_reader.c STAR-2.7.10a/source/htslib/tabix.1 STAR-2.7.10a/source/htslib/tabix.c STAR-2.7.10a/source/htslib/tbx.c STAR-2.7.10a/source/htslib/vcf.5 STAR-2.7.10a/source/htslib/vcf.c STAR-2.7.10a/source/htslib/vcf_sweep.c STAR-2.7.10a/source/htslib/vcfutils.c STAR-2.7.10a/source/insertSeqSA.cpp STAR-2.7.10a/source/insertSeqSA.h STAR-2.7.10a/source/mapThreadsSpawn.cpp STAR-2.7.10a/source/mapThreadsSpawn.h STAR-2.7.10a/source/opal/ STAR-2.7.10a/source/opal/LICENSE STAR-2.7.10a/source/opal/opal.cpp STAR-2.7.10a/source/opal/opal.h STAR-2.7.10a/source/opal/simde_avx2.h STAR-2.7.10a/source/outputSJ.cpp STAR-2.7.10a/source/outputSJ.h STAR-2.7.10a/source/parametersDefault STAR-2.7.10a/source/parametersDefault.xxd STAR-2.7.10a/source/readBarcodeLoad.h STAR-2.7.10a/source/readLoad.cpp STAR-2.7.10a/source/readLoad.h STAR-2.7.10a/source/samHeaders.cpp STAR-2.7.10a/source/samHeaders.h STAR-2.7.10a/source/serviceFuns.cpp STAR-2.7.10a/source/signalFromBAM.cpp STAR-2.7.10a/source/signalFromBAM.h STAR-2.7.10a/source/sjAlignSplit.cpp STAR-2.7.10a/source/sjAlignSplit.h STAR-2.7.10a/source/sjdbBuildIndex.cpp STAR-2.7.10a/source/sjdbBuildIndex.h STAR-2.7.10a/source/sjdbInsertJunctions.cpp STAR-2.7.10a/source/sjdbInsertJunctions.h STAR-2.7.10a/source/sjdbLoadFromFiles.cpp STAR-2.7.10a/source/sjdbLoadFromFiles.h STAR-2.7.10a/source/sjdbLoadFromStream.cpp STAR-2.7.10a/source/sjdbLoadFromStream.h STAR-2.7.10a/source/sjdbPrepare.cpp STAR-2.7.10a/source/sjdbPrepare.h STAR-2.7.10a/source/soloInputFeatureUMI.cpp STAR-2.7.10a/source/soloInputFeatureUMI.h STAR-2.7.10a/source/sortSuffixesBucket.h STAR-2.7.10a/source/stitchAlignToTranscript.cpp STAR-2.7.10a/source/stitchAlignToTranscript.h STAR-2.7.10a/source/stitchGapIndel.cpp STAR-2.7.10a/source/stitchWindowAligns.cpp STAR-2.7.10a/source/stitchWindowAligns.h STAR-2.7.10a/source/streamFuns.cpp STAR-2.7.10a/source/streamFuns.h STAR-2.7.10a/source/stringSubstituteAll.cpp STAR-2.7.10a/source/stringSubstituteAll.h STAR-2.7.10a/source/sysRemoveDir.cpp STAR-2.7.10a/source/sysRemoveDir.h STAR-2.7.10a/source/twoPassRunPass1.cpp STAR-2.7.10a/source/twoPassRunPass1.h default make make -C htslib lib-static make[1]: Entering directory '/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source/htslib' cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o kfunc.o kfunc.c cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o knetfile.o knetfile.c cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o kstring.o kstring.c cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o bgzf.o bgzf.c cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o faidx.o faidx.c cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o hfile.o hfile.c cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "0.0.1"' > version.h cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o hts.o hts.c hts.c: In function ‘hts_idx_init’: hts.c:522:63: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int’ changes value from ‘idx->z.last_bin = 4294967295’ to ‘-1’ [-Woverflow] 522 | idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu; | ^~~ cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o sam.o sam.c cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o synced_bcf_reader.o synced_bcf_reader.c cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o vcf_sweep.o vcf_sweep.c cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o tbx.o tbx.c cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o vcf.o vcf.c cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o vcfutils.o vcfutils.c cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o cram/cram_codecs.o cram/cram_codecs.c cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o cram/cram_decode.o cram/cram_decode.c cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o cram/cram_encode.o cram/cram_encode.c cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o cram/cram_index.o cram/cram_index.c cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o cram/cram_io.o cram/cram_io.c cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o cram/cram_samtools.o cram/cram_samtools.c cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o cram/cram_stats.o cram/cram_stats.c cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o cram/files.o cram/files.c cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o cram/mFILE.o cram/mFILE.c cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o cram/md5.o cram/md5.c cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o cram/open_trace_file.o cram/open_trace_file.c cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o cram/pooled_alloc.o cram/pooled_alloc.c cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o cram/sam_header.o cram/sam_header.c cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o cram/string_alloc.o cram/string_alloc.c cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o cram/thread_pool.o cram/thread_pool.c cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o cram/vlen.o cram/vlen.c cc -O2 -fPIC -fsigned-char -I. -DSAMTOOLS=1 -c -o cram/zfio.o cram/zfio.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/md5.o cram/open_trace_file.o cram/pooled_alloc.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o ranlib libhts.a make[1]: Leaving directory '/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source/htslib' echo BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall_multiMappers.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp twoPassRunPass1.cpp bam_cat.c BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall_multiMappers.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp twoPassRunPass1.cpp bam_cat.c 'rm' -f ./Depend.list g++ -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:04-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -MM BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall_multiMappers.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd htslib >> Depend.list g++: warning: parametersDefault.xxd: linker input file unused because linking not done g++: warning: htslib: linker input file unused because linking not done g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SoloFeature_collapseUMI_Graph.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SoloFeature_collapseUMIall_multiMappers.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra ParametersClip_initialize.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra ClipMate_clip.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra ClipCR4.cpp cd opal && \ g++ -c -I./ -std=c++11 -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra -O2 -fPIC -fsigned-char -mavx2 opal.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra ClipMate_clipChunk.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra ClipMate_initialize.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SoloFeature_loadRawMatrix.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SoloFeature_emptyDrops_CR.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra soloInputFeatureUMI.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SoloFeature_countSmartSeq.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SoloFeature_redistributeReadsByCB.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SoloFeature_quantTranscript.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SoloFeature_sumThreads.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SoloFeature_countVelocyto.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SoloFeature_countCBgeneUMI.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra Transcriptome_classifyAlign.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SoloFeature_cellFiltering.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SoloFeature_statsOutput.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra bamSortByCoordinate.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SoloBarcode.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra ParametersSolo.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SoloRead.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SoloRead_record.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SoloReadBarcode.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SoloReadBarcode_getCBandUMI.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SoloBarcode_extractBarcode.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SoloReadFeature.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SoloReadFeature_record.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SoloReadFeature_inputRecords.cpp SoloReadFeature_inputRecords.cpp: In member function ‘void SoloReadFeature::inputRecords(unsigned int**, unsigned int, std::vector&, std::vector&, SoloReadFlagClass&, std::vector&, std::vector&)’: SoloReadFeature_inputRecords.cpp:21:12: warning: unused variable ‘nReadsIn’ [-Wunused-variable] 21 | uint64 nReadsIn = 0; | ^~~~~~~~ g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra Solo.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SoloFeature.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SoloFeature_outputResults.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SoloFeature_processRecords.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SoloFeature_addBAMtags.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra ReadAlign_transformGenome.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra Genome_transformGenome.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra Transcript_convertGenomeCigar.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra twoPassRunPass1.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra samHeaders.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra Genome_genomeLoad.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra Genome_genomeOutLoad.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra Transcript_transformGenome.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra ReadAlign_outputSpliceGraphSAM.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SpliceGraph.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SpliceGraph_swScoreSpliced.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SpliceGraph_swTraceBack.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SpliceGraph_findSuperTr.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra sjAlignSplit.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra GTF.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra GTF_transcriptGeneSJ.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra GTF_superTranscript.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SuperTranscriptome.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra ReadAlign_outputAlignments.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra ReadAlign.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra STAR.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SharedMemory.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra PackedArray.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SuffixArrayFuns.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra Parameters.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra Parameters_samAttributes.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra InOutStreams.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SequenceFuns.cpp g++ 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Transcript_variationAdjust.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra Variation.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra ReadAlign_waspMap.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra ReadAlign_storeAligns.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' 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ReadAlign_outputTranscriptSJ.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra ReadAlign_outputTranscriptCIGARp.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra ReadAlign_assignAlignToWindow.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 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ReadAlign_chimericDetectionOld.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra ReadAlign_chimericDetectionOldOutput.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra ChimericDetection.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra ChimericDetection_chimericDetectionMult.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 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-D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra ChimericAlign_chimericJunctionOutput.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra ChimericAlign_chimericBAMoutput.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra ChimericAlign_chimericStitching.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra Genome_genomeGenerate.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra genomeParametersWrite.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra genomeScanFastaFiles.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra genomeSAindex.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra Genome_insertSequences.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra insertSeqSA.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra funCompareUintAndSuffixes.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra funCompareUintAndSuffixesMemcmp.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra TimeFunctions.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra ErrorWarning.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra streamFuns.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra stringSubstituteAll.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra Transcriptome.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra Transcriptome_quantAlign.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra Transcriptome_geneFullAlignOverlap.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra ReadAlign_quantTranscriptome.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra Quantifications.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra Transcriptome_geneCountsAddAlign.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra sjdbLoadFromFiles.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra sjdbLoadFromStream.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra sjdbPrepare.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra sjdbBuildIndex.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra sjdbInsertJunctions.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra mapThreadsSpawn.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra Parameters_readFilesInit.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra Parameters_readSAMheader.cpp g++ -c -O2 -fPIC -fsigned-char bam_cat.c g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra serviceFuns.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra BAMoutput.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra BAMfunctions.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra ReadAlign_alignBAM.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra BAMbinSortByCoordinate.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra signalFromBAM.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra bamRemoveDuplicates.cpp g++ -c -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra BAMbinSortUnmapped.cpp g++ -o STAR -O2 -fPIC -fsigned-char -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2022-06-03T13:35:19-00:00 darkstar.example.net:/usr/src/slapt-src/academic/STAR/STAR-2.7.10a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall_multiMappers.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz Parameters_openReadsFiles.cpp: In member function ‘void Parameters::openReadsFiles()’: Parameters_openReadsFiles.cpp:25:20: warning: variable ‘imate’ might be clobbered by ‘longjmp’ or ‘vfork’ [-Wclobbered] 25 | for (uint imate=0;imate