Include dependency graph for computeStats.h:
Go to the source code of this file.
Classes | |
| struct | Stats |
Functions | |
| vector< unsigned > | extractBarcodesCountsPerRegion (BamReader &reader, vector< string > regionsList, unsigned numberOfRegions) |
| vector< unsigned > | extractCommonBarcodesCounts (BamReader &reader, vector< string > regionsList, unsigned numberOfRegions) |
| pair< vector< unsigned >, vector< unsigned > > | extractBarcodesAndCommonBarcodesCounts (string bamFile, vector< string > regionsList, unsigned numberOfRegions, unsigned nbThreads=1) |
| Stats | extractGlobalStats (string bamFile, unsigned nbThreads=1) |
Function Documentation
◆ extractBarcodesAndCommonBarcodesCounts()
| pair<vector<unsigned>, vector<unsigned> > extractBarcodesAndCommonBarcodesCounts | ( | string | bamFile, |
| vector< string > | regionsList, | ||
| unsigned | numberOfRegions, | ||
| unsigned | nbThreads = 1 |
||
| ) |
Extract the number of barcodes from a random list of regions and the number of common barcodes between adjacent regions of these regions.
- Parameters
-
bamFile BAM file to extract stats from regionsList the list of all regions of the reference genome numberOfRegions number of adjacent windows to consider 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 pair composed of sorted list containing the number of barcodes of the randomly selected regions and a sorted list containing the number of common barcodes between adjacent windows of the selected windows
◆ extractBarcodesCountsPerRegion()
| vector<unsigned> extractBarcodesCountsPerRegion | ( | BamReader & | reader, |
| vector< string > | regionsList, | ||
| unsigned | numberOfRegions | ||
| ) |
Extract the number of barcodes from a random list of regions.
- Parameters
-
reader BamReader open on the desired BAM file regionsList the list of all regions of the reference genome numberOfRegions number of regions to extract barcodes from
- Returns
- A sorted list containing the number of barcodes of the randomly selected regions
◆ extractCommonBarcodesCounts()
| vector<unsigned> extractCommonBarcodesCounts | ( | BamReader & | reader, |
| vector< string > | regionsList, | ||
| unsigned | numberOfRegions | ||
| ) |
Extract the number of common barcodes between random adjacent regions.
- Parameters
-
reader BamReader open on the desired BAM file regionsList the list of all regions of the reference genome numberOfRegions number of adjacent windows to consider
- Returns
- A sorted list containing the number of common barcodes between the randomly selected adjacent regions
◆ extractGlobalStats()
| Stats extractGlobalStats | ( | string | bamFile, |
| unsigned | nbThreads = 1 |
||
| ) |
Extract global stats (number of barcodes, number of mapped reads, number of reads for each barcode).
- Parameters
-
bamFile BAM file to extract stats from nbThreads number of threads to use, set to 1 by default
- Exceptions
-
ios_base::failure thrown if bamFile or its associated index, or if regions could not be open runtime_error thrown if bamFile could not be seeked
- Returns
- A structure describing the global stats of the BAM file
