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Macros | |
| #define | BUFSIZE 134217728 |
Typedefs | |
| typedef robin_hood::unordered_map< barcode, vector< int64_t > > | BarcodesIndex |
Functions | |
| BarcodesIndex | indexBarcodesFromFastq (string fastqFile, unsigned nbThreads=1) |
| BarcodesIndex | indexBarcodesFromFastqGz (string fastqFile, unsigned nbThreads=1) |
| void | saveBarcodesIndex (BarcodesIndex &index, string file) |
| BarcodesIndex | loadBarcodesIndex (string file) |
Macro Definition Documentation
◆ BUFSIZE
| #define BUFSIZE 134217728 |
Definition at line 10 of file indexManagementFastq.h.
Typedef Documentation
◆ BarcodesIndex
| typedef robin_hood::unordered_map<barcode, vector<int64_t> > BarcodesIndex |
Definition at line 12 of file indexManagementFastq.h.
Function Documentation
◆ indexBarcodesFromFastq()
| BarcodesIndex indexBarcodesFromFastq | ( | string | fastqFile, |
| unsigned | nbThreads = 1 |
||
| ) |
Index the offsets of the barcodes contained in a given fastq file.
- Parameters
-
fastqFile fastq file to build the index from nbThreads number of threads to use, set to 1 by default
- Exceptions
-
ios_base::failure thrown if fastqFile could not be open
- Returns
- the barcode index associating barcodes to the set of offsets they occur at
◆ indexBarcodesFromFastqGz()
| BarcodesIndex indexBarcodesFromFastqGz | ( | string | fastqFile, |
| unsigned | nbThreads = 1 |
||
| ) |
Index the offsets of the barcodes contained in a given gzipped fastq file.
- Parameters
-
fastqFile gzipped fastq file to build the index from nbThreads number of threads to use, set to 1 by default
- Exceptions
-
ios_base::failure thrown if fastqFile could not be open
- Returns
- the barcode index associating barcodes to the set of offsets they occur at
◆ loadBarcodesIndex()
| BarcodesIndex loadBarcodesIndex | ( | string | file | ) |
Load the barcode index stored in a given file.
- Parameters
-
file file where the barcode index is stored
- Exceptions
-
ios_base::failure thrown if file could not be open
- Returns
- the barcode index filled with the data contained in the file
◆ saveBarcodesIndex()
| void saveBarcodesIndex | ( | BarcodesIndex & | index, |
| string | file | ||
| ) |
Save the content of the barcode index in a given file.
- Parameters
-
index barcode offsets index to save
- Exceptions
-
ios_base::failure thrown if file could not be open
- Parameters
-
file file where to store the index
