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Function Documentation
◆ extractBarcodesBitsFromBAM()
| robin_hood::unordered_set<barcode> extractBarcodesBitsFromBAM | ( | string | bamFile, |
| unsigned | nbThreads = 1 |
||
| ) |
Extract all the barcodes of a given BAM file, in binary representation.
- Parameters
-
bamFile bamFile BAM file to extract barcodes from nbThreads number of threads to use, set to 1 by default
- Exceptions
-
ios_base::failure thrown if bamFile or its associated index could not be open
- Returns
- a set containing the barcodes present in the BAM file, in binary representation
◆ extractBarcodesBitsFromBAMWithDuplicates()
| vector<barcode> extractBarcodesBitsFromBAMWithDuplicates | ( | string | bamFile, |
| unsigned | nbThreads = 1 |
||
| ) |
Extract all the barcodes of a given BAM file, in binary representation, including duplicates.
- Parameters
-
bamFile bamFile BAM file to extract barcodes from nbThreads number of threads to use, set to 1 by default
- Exceptions
-
ios_base::failure thrown if bamFile or its associated index could not be open
- Returns
- a vector containing the barcodes present in the BAM file, in binary representation
◆ extractBarcodesBitsFromRegion()
| robin_hood::unordered_set<barcode> extractBarcodesBitsFromRegion | ( | string | bamFile, |
| string | region | ||
| ) |
Extract the barcodes of a given region, in binary representation.
- Parameters
-
reader bamFile BAM file to extract barcodes from region region of interest
- Exceptions
-
runtime_error thrown if region could not be converted to a BamRegion or jumped to
- Returns
- a set containing the barcodes present in the region, in binary representation
◆ extractBarcodesBitsFromRegion_BamReader()
| robin_hood::unordered_set<barcode> extractBarcodesBitsFromRegion_BamReader | ( | BamReader & | reader, |
| string | region | ||
| ) |
Extract the barcodes of a given region, in binary representation.
- Parameters
-
reader BamReader open on the desired BAM file region region of interest
- Exceptions
-
runtime_error thrown if region could not be converted to a BamRegion or jumped to
- Returns
- a set containing the barcodes present in the region
◆ extractBarcodesBitsFromRegionWithDuplicates()
| vector<barcode> extractBarcodesBitsFromRegionWithDuplicates | ( | string | bamFile, |
| string | region | ||
| ) |
Extract the barcodes of a given region, in binary representation, including duplicates.
- Parameters
-
reader bamFile BAM file to extract barcodes from region region of interest
- Exceptions
-
ios_base::failure thrown if bamFile or its associated index could not be open
- Returns
- a vector containing the barcodes present in the region, in binary representation
◆ extractBarcodesBitsFromRegionWithDuplicates_BamReader()
| vector<barcode> extractBarcodesBitsFromRegionWithDuplicates_BamReader | ( | BamReader & | reader, |
| string | region | ||
| ) |
Extract the barcodes of a given region, in binary representation, including duplicates.
- Parameters
-
reader BamReader open on the desired BAM file region region of interest
- Exceptions
-
runtime_error thrown if region could not be converted to a BamRegion or jumped to
- Returns
- a vector containing the barcodes present in the region
◆ extractBarcodesSeqsFromBAM()
| robin_hood::unordered_set<string> extractBarcodesSeqsFromBAM | ( | string | bamFile, |
| unsigned | nbThreads = 1 |
||
| ) |
Extract all the barcodes of a given BAM file, in string representation.
- Parameters
-
bamFile bamFile BAM file to extract barcodes from nbThreads number of threads to use, set to 1 by default
- Exceptions
-
ios_base::failure thrown if bamFile or its associated index could not be open
- Returns
- a set containing the barcodes present in the BAM file, in string representation
◆ extractBarcodesSeqsFromBAMWithDuplicates()
| vector<string> extractBarcodesSeqsFromBAMWithDuplicates | ( | string | bamFile, |
| unsigned | nbThreads = 1 |
||
| ) |
Extract all the barcodes of a given BAM file, in string representation, including duplicates.
- Parameters
-
bamFile bamFile BAM file to extract barcodes from nbThreads number of threads to use, set to 1 by default
- Exceptions
-
ios_base::failure thrown if bamFile or its associated index could not be open
- Returns
- a vector containing the barcodes present in the BAM file, in string representation
◆ extractBarcodesSeqsFromRegion()
| robin_hood::unordered_set<string> extractBarcodesSeqsFromRegion | ( | string | bamFile, |
| string | region | ||
| ) |
Extract the barcodes of a given region, in string representation.
- Parameters
-
reader bamFile BAM file to extract barcodes from region region of interest
- Exceptions
-
runtime_error thrown if region could not be converted to a BamRegion or jumped to
- Returns
- a set containing the barcodes present in the region, in binary string
◆ extractBarcodesSeqsFromRegion_BamReader()
| robin_hood::unordered_set<string> extractBarcodesSeqsFromRegion_BamReader | ( | BamReader & | reader, |
| string | region | ||
| ) |
Extract the barcodes of a given region, in string representation.
- Parameters
-
reader BamReader open on the desired BAM file region region of interest
- Exceptions
-
runtime_error thrown if region could not be converted to a BamRegion or jumped to
- Returns
- a set containing the barcodes present in the region
◆ extractBarcodesSeqsFromRegionWithDuplicates()
| vector<string> extractBarcodesSeqsFromRegionWithDuplicates | ( | string | bamFile, |
| string | region | ||
| ) |
Extract the barcodes of a given region, in string representation, including duplicates.
- Parameters
-
reader bamFile BAM file to extract barcodes from region region of interest
- Exceptions
-
ios_base::failure thrown if bamFile or its associated index could not be open
- Returns
- a vector containing the barcodes present in the region, in binary string
◆ extractBarcodesSeqsFromRegionWithDuplicates_BamReader()
| vector<string> extractBarcodesSeqsFromRegionWithDuplicates_BamReader | ( | BamReader & | reader, |
| string | region | ||
| ) |
Extract the barcodes of a given region, in string representation, including duplicates.
- Parameters
-
reader BamReader open on the desired BAM file region region of interest
- Exceptions
-
runtime_error thrown if region could not be converted to a BamRegion or jumped to
- Returns
- a vector containing the barcodes present in the region
