readsToGAlignments: Convert reads to GAlignments.
In GoogleGenomics: R Client for Google Genomics API

Description Usage Arguments Value Examples

Note that the Global Alliance for Genomics and Health API uses a 0-based coordinate system. For more detail, please see GA4GH discussions such as the following:

1	readsToGAlignments(reads, oneBasedCoord = TRUE, slStyle = "UCSC")

`reads`	A list of R objects corresponding to the JSON objects returned by the Google Genomics Reads API.
`oneBasedCoord`	Convert genomic positions to 1-based coordinates.
`slStyle`	The style for seqnames (chrN or N or...). Default is UCSC.

GAlignments

# Authenticated on package load from the env variable GOOGLE_API_KEY.
alignments1 <- getReads(converter=readsToGAlignments)
summary(alignments1)
alignments2 <- readsToGAlignments(getReads())
print(identical(alignments1, alignments2))