internal: Count bases in cigar string
In mskilab/bambi: R to query barcode indices on bam files
Description
Usage
Arguments
Value
Description
Counts the total number of bases, per cigar, that fall into D, I, M, S categories.
countCigar() makes no distinction between, for instance 1S2M2S, 2S2M1S, or 3S2M
Shortcut function in create_granges
Usage
1
2
3
countCigar(cigar)
bamflag(reads)
Arguments
cigar
character vector of cigar strings
reads
data.table holding the reads
Value
a 4-column, length(cigar)-row matrix with the total counts for each type
matrix of bits from BAM flags
mskilab/bambi documentation built on May 14, 2019, 4:04 a.m.
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Description Usage Arguments Value
Description
Counts the total number of bases, per cigar, that fall into D, I, M, S categories. countCigar() makes no distinction between, for instance 1S2M2S, 2S2M1S, or 3S2M
Shortcut function in create_granges
Usage
1 2 3 | countCigar(cigar)
bamflag(reads)
|
Arguments
cigar |
character vector of cigar strings |
reads |
data.table holding the reads |
Value
a 4-column, length(cigar)-row matrix with the total counts for each type
matrix of bits from BAM flags
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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