Hi,
Does anybody know of an R function that takes a decimal number as input, the FLAG number from a SAM file, and outputs a list of text stating whether the read has multiple alignments, is properly aligned, is mapped, etc.?
It should not be too hard to code, but if it is already present in some Bioconductor package, I would rather use that.
Thanks.
Best, C.
•
written
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biomagician
https://rdrr.io/github/jefferys/SamSeq/
> library(SamSeq)
> samFlags(1024)
SUPPLEMENTARY_ALIGNMENT DUPLICATE_READ READ_FAILS_VENDOR_QC NOT_PRIMARY_ALIGNMENT
FALSE TRUE FALSE FALSE
SECOND_OF_PAIR FIRST_OF_PAIR MATE_REVERSE_STRAND READ_REVERSE_STRAND
FALSE FALSE FALSE FALSE
MATE_UNMAPPED READ_UNMAPPED PROPER_PAIR READ_PAIRED
FALSE FALSE FALSE FALSE
> samFlags(228)[samFlags(228)==1]
SECOND_OF_PAIR FIRST_OF_PAIR MATE_REVERSE_STRAND READ_UNMAPPED
TRUE TRUE TRUE TRUE
> samFlags(2056)[samFlags(2056)==1]
SUPPLEMENTARY_ALIGNMENT MATE_UNMAPPED
TRUE TRUE
> samFlags(128)[samFlags(128)==1]
SECOND_OF_PAIR
TRUE
Reverse flag search:
> samFlags("SUPPLEMENTARY_ALIGNMENT")
[1] 2048
> samFlags(c("SUPPLEMENTARY_ALIGNMENT","MATE_UNMAPPED"))
[1] 2056
library(Rsamtools)
bamFlagAsBitMatrix( as.integer (1024))
FLAG_BITNAMES[ as.logical( bamFlagAsBitMatrix( as.integer(1024)))]
Tip of the day: to save typing, declare integer type with the L suffix as in 1024L, instead of as.integer(1024).
https://www.rdocumentation.org/packages/Rsamtools/versions/1.24.0/topics/ScanBamParam
This doesn't answer 100% your question but ScanBamParam() / ScanBamFlag can parse a SAM file and extract reads with certain features (isProperPair, isPaired, ...)
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