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Typedefs | |
| typedef robin_hood::unordered_map< barcode, vector< int64_t > > | BarcodesOffsetsIndex |
| typedef robin_hood::unordered_map< barcode, vector< pair< int32_t, int32_t > > > | BarcodesPositionsIndex |
Functions | |
| BarcodesPositionsIndex | indexBarcodesPositionsFromBam (string bamFile, bool primary, unsigned quality, unsigned nbThreads=1) |
| void | saveBarcodesPositionsIndex (BarcodesPositionsIndex &index, string file) |
| BarcodesPositionsIndex | loadBarcodesPositionsIndex (string file) |
| BarcodesOffsetsIndex | indexBarcodesOffsetsFromBam (string bamFile, bool primary, unsigned quality, unsigned nbThreads=1) |
| void | saveBarcodesOffsetsIndex (BarcodesOffsetsIndex &index, string file) |
| BarcodesOffsetsIndex | loadBarcodesOffsetsIndex (string file) |
Typedef Documentation
◆ BarcodesOffsetsIndex
| typedef robin_hood::unordered_map<barcode, vector<int64_t> > BarcodesOffsetsIndex |
Definition at line 12 of file indexManagementBam.h.
◆ BarcodesPositionsIndex
| typedef robin_hood::unordered_map<barcode, vector<pair<int32_t, int32_t> > > BarcodesPositionsIndex |
Definition at line 14 of file indexManagementBam.h.
Function Documentation
◆ indexBarcodesOffsetsFromBam()
| BarcodesOffsetsIndex indexBarcodesOffsetsFromBam | ( | string | bamFile, |
| bool | primary, | ||
| unsigned | quality, | ||
| unsigned | nbThreads = 1 |
||
| ) |
Index the offsets of the barcodes contained in a given BAM file.
- Parameters
-
reader bamFile BAM file to build the index from primary whether to only index primary alignments or not quality minimum quality to index an alignment nbThreads number of threads to use, set to 1 by default
- Exceptions
-
runtime_error thrown if bamFile could not be seeked ios_base::failure thrown if bamFile or its associated index could not be open
- Returns
- the barcode index associating barcodes to the set of offsets they occur at
◆ indexBarcodesPositionsFromBam()
| BarcodesPositionsIndex indexBarcodesPositionsFromBam | ( | string | bamFile, |
| bool | primary, | ||
| unsigned | quality, | ||
| unsigned | nbThreads = 1 |
||
| ) |
Index the (chromosome, begPosition) pairs of the barcodes contained in a given BAM file.
- Parameters
-
reader bamFile BAM file to build the index from primary whether to only index primary alignments or not quality minimum quality to index an alignment 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
- the barcode positions index associating barcodes to the set of (chromosome, begPosition) pairs they occur at
◆ loadBarcodesOffsetsIndex()
| BarcodesOffsetsIndex loadBarcodesOffsetsIndex | ( | string | file | ) |
Load the barcode index stored in a given file.
- Parameters
-
file file where the barcode offsets index is stored
- Exceptions
-
ios_base::failure thrown if file could not be open
- Returns
- the barcode offsets index filled with the data contained in the file
◆ loadBarcodesPositionsIndex()
| BarcodesPositionsIndex loadBarcodesPositionsIndex | ( | string | file | ) |
Load the barcode positions index stored in a given file.
- Parameters
-
file file where the barcode positions index is stored
- Exceptions
-
ios_base::failure thrown if file could not be open
- Returns
- the barcode positions index filled with the data contained in the file
◆ saveBarcodesOffsetsIndex()
| void saveBarcodesOffsetsIndex | ( | BarcodesOffsetsIndex & | index, |
| string | file | ||
| ) |
Save the content of the barcode index in a given file.
- Parameters
-
BarcodesOffsetsIndex barcode offsets index to save
- Exceptions
-
ios_base::failure thrown if file could not be open
- Parameters
-
file file where to store the index
◆ saveBarcodesPositionsIndex()
| void saveBarcodesPositionsIndex | ( | BarcodesPositionsIndex & | index, |
| string | file | ||
| ) |
Save the content of the barcode positions index in a given file.
- Parameters
-
BarcodesPositionsIndex barcode positions index to save
- Exceptions
-
ios_base::failure thrown if file could not be open
- Parameters
-
file file where to store the index
