- b -

• buildGzIndex() : gzIndex.h
• buildGzIndex_Stream() : gzIndex.h

- c -

• compareContig() : barcodesComparison.h
• compareContig_BamReader() : barcodesComparison.h
• compareContigs() : barcodesComparison.h
• compareRegions() : barcodesComparison.h
• computeCommonBarcodesCounts() : barcodesComparison.h
• computePairwiseCommonBarcounts() : barcodesComparison.h
• convertToSam() : utils.h
• countCommonBarcodes() : barcodesComparison.h

- d -

• deserializeGzIndex() : gzIndex.h
• determineSequencingTechnology() : utils.h

- e -

• extract() : gzIndex.h
• extract_Stream() : gzIndex.h
• extractBarcodesAndCommonBarcodesCounts() : computeStats.h
• extractBarcodesBitsFromBAM() : barcodesExtraction.h
• extractBarcodesBitsFromBAMWithDuplicates() : barcodesExtraction.h
• extractBarcodesBitsFromRegion() : barcodesExtraction.h
• extractBarcodesBitsFromRegion_BamReader() : barcodesExtraction.h
• extractBarcodesBitsFromRegionWithDuplicates() : barcodesExtraction.h
• extractBarcodesBitsFromRegionWithDuplicates_BamReader() : barcodesExtraction.h
• extractBarcodesCountsPerRegion() : computeStats.h
• extractBarcodesSeqsFromBAM() : barcodesExtraction.h
• extractBarcodesSeqsFromBAMWithDuplicates() : barcodesExtraction.h
• extractBarcodesSeqsFromRegion() : barcodesExtraction.h
• extractBarcodesSeqsFromRegion_BamReader() : barcodesExtraction.h
• extractBarcodesSeqsFromRegionWithDuplicates() : barcodesExtraction.h
• extractBarcodesSeqsFromRegionWithDuplicates_BamReader() : barcodesExtraction.h
• extractCommonBarcodesCounts() : computeStats.h
• extractFastqReadFromOffset() : gzIndex.h
• extractGlobalStats() : computeStats.h
• extractRegions() : utils.h
• extractRegionsList() : utils.h

- f -

• freeGzIndex() : gzIndex.h

- i -

• indexBarcodesFromFastq() : indexManagementFastq.h
• indexBarcodesFromFastqGz() : indexManagementFastq.h
• indexBarcodesOffsetsFromBam() : indexManagementBam.h
• indexBarcodesPositionsFromBam() : indexManagementBam.h
• isValidBarcode() : utils.h

- l -

• loadBarcodesIndex() : indexManagementFastq.h
• loadBarcodesOffsetsIndex() : indexManagementBam.h
• loadBarcodesPositionsIndex() : indexManagementBam.h

- r -

• retrieveAlignmentsWithBarcode() : alignmentsRetrieval.h
• retrieveAlignmentsWithBarcode_BamReader() : alignmentsRetrieval.h
• retrieveAlignmentsWithBarcodeBits() : alignmentsRetrieval.h
• retrieveAlignmentsWithBarcodeBits_BamReader() : alignmentsRetrieval.h
• retrieveAlignmentsWithBarcodes() : alignmentsRetrieval.h
• retrieveAlignmentsWithBarcodes_BamReader() : alignmentsRetrieval.h
• retrieveNucleotidesContent() : utils.h
• retrieveReadsWithBarcode() : readsRetrieval.h
• retrieveReadsWithBarcode_Gzip() : readsRetrieval.h
• retrieveReadsWithBarcode_Gzip_Stream_Index() : readsRetrieval.h
• retrieveReadsWithBarcode_Stream() : readsRetrieval.h
• retrieveReadsWithBarcodeBits() : readsRetrieval.h
• retrieveReadsWithBarcodeBits_Gzip() : readsRetrieval.h
• retrieveReadsWithBarcodeBits_Gzip_Stream_Index() : readsRetrieval.h
• retrieveReadsWithBarcodeBits_Stream() : readsRetrieval.h
• retrieveReadsWithBarcodes() : readsRetrieval.h
• retrieveReadsWithBarcodes_Gzip() : readsRetrieval.h
• retrieveReadsWithBarcodes_Gzip_Stream_Index() : readsRetrieval.h
• retrieveReadsWithBarcodes_Stream() : readsRetrieval.h

- s -

• saveBarcodesIndex() : indexManagementFastq.h
• saveBarcodesOffsetsIndex() : indexManagementBam.h
• saveBarcodesPositionsIndex() : indexManagementBam.h
• serializeGzIndex() : gzIndex.h
• splitString() : utils.h
• stringToBamRegion() : utils.h
• stringToBarcode() : utils.h
• subcommandCompare() : compare.h
• subcommandExtract() : extract.h
• subcommandHelp() : help.h
• subcommandIndexBam() : indexBam.h
• subcommandIndexFastq() : indexFastq.h
• subcommandQueryBam() : queryBam.h
• subcommandQueryFastq() : queryFastq.cpp , queryFastq.h
• subcommandStats() : stats.h