readsToGAlignments: Convert reads to GAlignments.
In adamstruck/ga4ghr: R Client for GA4GH 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 GA4GH Reads API.
`oneBasedCoord`	Convert genomic positions to 1-based coordinates.
`slStyle`	The style for seqnames (chrN or N or...). Default is UCSC.

GAlignments

alignments1 <- searchReads(converter = readsToGAlignments)
summary(alignments1)
alignments2 <- readsToGAlignments(searchReads())
print(identical(alignments1, alignments2))