alignGapList read gap-site data from single BAM-files (given as
bamReader) and return a
getGapSites reads data for one seqid (given as 1-based numeric value).
alignGapList reads the whole BAM-file. The functions test for opened reader and initialized index.
bamReader (rbamtools). An opened instance of
Numeric. 1-based index of reference sequence for which gap-sites are to be read.
Numeric. Default: 1. Determines start value for
getGapSites internally calls
alignGapList internally calls
rbamtools::bamGapList. 'nProbes' values are set to 1.
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