Include dependency graph for alignmentsRetrieval.h:
Go to the source code of this file.
Functions | |
| vector< BamAlignment > | retrieveAlignmentsWithBarcodeBits_BamReader (BamReader &reader, BarcodesOffsetsIndex &BarcodesOffsetsIndex, barcode b) |
| vector< BamAlignment > | retrieveAlignmentsWithBarcode_BamReader (BamReader &reader, BarcodesOffsetsIndex &BarcodesOffsetsIndex, string bc) |
| vector< BamAlignment > | retrieveAlignmentsWithBarcode (string bamFile, BarcodesOffsetsIndex &BarcodesOffsetsIndex, string bc) |
| vector< BamAlignment > | retrieveAlignmentsWithBarcodeBits (string bamFile, BarcodesOffsetsIndex &BarcodesOffsetsIndex, barcode bc) |
| vector< BamAlignment > | retrieveAlignmentsWithBarcodes_BamReader (BamReader &reader, BarcodesOffsetsIndex &BarcodesOffsetsIndex, string barcodesList) |
| vector< BamAlignment > | retrieveAlignmentsWithBarcodes (string bamFile, BarcodesOffsetsIndex &BarcodesOffsetsIndex, string barcodesList, unsigned nbThreads=1) |
Function Documentation
◆ retrieveAlignmentsWithBarcode()
| vector<BamAlignment> retrieveAlignmentsWithBarcode | ( | string | bamFile, |
| BarcodesOffsetsIndex & | BarcodesOffsetsIndex, | ||
| string | bc | ||
| ) |
Retrieve all the alignments that share a given barcode, in a given BAM file. A barcode index of the BAM must be available.
- Parameters
-
bamFile BAM file to extract alignments from BarcodesOffsetsIndex barcode offsets index of the BAM file bc barcode of interest
- Returns
- a vector containing all the alignments sharing the barcode of interest
◆ retrieveAlignmentsWithBarcode_BamReader()
| vector<BamAlignment> retrieveAlignmentsWithBarcode_BamReader | ( | BamReader & | reader, |
| BarcodesOffsetsIndex & | BarcodesOffsetsIndex, | ||
| string | bc | ||
| ) |
Retrieve all the alignments that share a given barcode, in a given BAM file. A barcode index of the BAM must be available.
- Parameters
-
reader BamReader open on the desired BAM file BarcodesOffsetsIndex barcode offsets index of the BAM file bc barcode of interest
- Returns
- a vector containing all the alignments sharing the barcode of interest
◆ retrieveAlignmentsWithBarcodeBits()
| vector<BamAlignment> retrieveAlignmentsWithBarcodeBits | ( | string | bamFile, |
| BarcodesOffsetsIndex & | BarcodesOffsetsIndex, | ||
| barcode | bc | ||
| ) |
Retrieve all the alignments that share a given barcode, in a given BAM file. A barcode index of the BAM must be available.
- Parameters
-
bamFile BAM file to extract alignments from BarcodesOffsetsIndex barcode offsets index of the BAM file bc barcode of interest, in binary representation
- Exceptions
-
ios_base::failure thrown if bamFile or its associated index could not be open
- Returns
- a vector containing all the alignments sharing the barcode of interest
◆ retrieveAlignmentsWithBarcodeBits_BamReader()
| vector<BamAlignment> retrieveAlignmentsWithBarcodeBits_BamReader | ( | BamReader & | reader, |
| BarcodesOffsetsIndex & | BarcodesOffsetsIndex, | ||
| barcode | b | ||
| ) |
Retrieve all the alignments that share a given barcode, in a given BAM file. A barcode index of the BAM must be available.
- Parameters
-
reader BamReader open on the desired BAM file BarcodesOffsetsIndex barcode offsets index of the BAM file b barcode of interest, in binary representation
- Exceptions
-
runtime_error thrown if a given offset of the file where the barcode appears could not be seeked
- Returns
- a vector containing all the alignments sharing the barcode of interest
◆ retrieveAlignmentsWithBarcodes()
| vector<BamAlignment> retrieveAlignmentsWithBarcodes | ( | string | bamFile, |
| BarcodesOffsetsIndex & | BarcodesOffsetsIndex, | ||
| string | barcodesList, | ||
| unsigned | nbThreads = 1 |
||
| ) |
Retrieve all the alignments that share a barcode appearing in the list of a given file
- Parameters
-
bamFile BAM file to extract alignments from BarcodesOffsetsIndex barcode offsets index of the BAM file barcodesList file containing the list of barcodes of interest, with one barcode per line nbThreads number of threads to use, set to 1 by default
- Exceptions
-
ios_base::failure thrown if bamFile or its associated index, or if barcodesList could not be open
- Returns
- a vector containing all the alignments with the barcodes of interest
◆ retrieveAlignmentsWithBarcodes_BamReader()
| vector<BamAlignment> retrieveAlignmentsWithBarcodes_BamReader | ( | BamReader & | reader, |
| BarcodesOffsetsIndex & | BarcodesOffsetsIndex, | ||
| string | barcodesList | ||
| ) |
Retrieve all the alignments that share a barcode appearing in the list of a given file
- Parameters
-
in stream open on the BAM fastq file BarcodesOffsetsIndex barcode offsets index of the BAM file barcodesList file containing the list of barcodes of interest, with one barcode per line
- Exceptions
-
ios_base::failure thrown if barcodesList could not be open
- Returns
- a vector containing all the alignments with the barcodes of interest
