Read paired end bam file by yield size
tx_load_bam.Rd
Reads a file in BAM format by blocks of lines equal to a yield size, either automatically calculated or specified by the user, and loads it as a GenomicAlignments object.
Usage
tx_load_bam(
file,
pairedEnd,
yieldSize = 1e+05,
scanFlag = "default",
loadSeq = FALSE,
strandMode = 1,
verbose = TRUE
)
Arguments
- file
character. Path to the file to read
- pairedEnd
logical. Set to FALSE if reads in BAM file are single-end, set to TRUE if reads are paired-end.
- yieldSize
numeric. Number of reads to be processed at a time
- scanFlag
integer. Flag used to filter reads. See
ScanBamParam
- loadSeq
logical. Set to TRUE for loading the sequences contained in the BAM file
- strandMode
numeric.
1 (default): Strand of the pair is that of its first alignment: Directional Illumina (Ligation), Standard SOLiD. (Single-end No change in strand)
2: strand of the pair is strand of its last alignment: dUTP, NSR, NNSR, Illumina stranded TruSeq PE protocol. (Single-end: Change to inverse strand)
0: strand of the pair is set to '*' (unspecified). This mode is no longer supported by
tx_reads
() .
More info:
GAlignmentPairs-class
.- verbose
logical. Set to FALSE to show less information.
Examples
# Loading in-package BAM file
bamFile <- system.file("extdata", "example_hg19.bam", package = "txtools")
hg19_bam <- tx_load_bam(bamFile, pairedEnd = TRUE, loadSeq = TRUE, verbose = TRUE)
#> Reading number of records in file
#> 5061 number of BAM records
#> Loading BAM file
#>
|
| | 0%
|
|======================================================================| 100%
#> 0 reads filtered out for empty sequence field
#> 2530 Reads succesfully loaded
#> Dumped ambiguous reads: 0
summary(hg19_bam)
#> [1] "GAlignmentPairs object of length 2530 with 0 metadata columns"