This file is indexed.

/usr/lib/R/site-library/GenomicAlignments/INDEX is in r-bioc-genomicalignments 1.0.6-1.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

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GAlignmentPairs-class   GAlignmentPairs objects
GAlignments-class       GAlignments objects
GAlignmentsList-class   GAlignmentsList objects
GappedReads-class       (Legacy) GappedReads objects
OverlapEncodings-class
                        OverlapEncodings objects
cigar-utils             CIGAR utility functions
coverage-methods        Coverage of a GAlignments or GAlignmentPairs
                        object
encodeOverlaps-methods
                        Encode the overlaps between RNA-seq reads and
                        the transcripts of a gene model
findCompatibleOverlaps-methods
                        Finding hits between reads and transcripts that
                        are _compatible_ with the splicing of the
                        transcript
findMateAlignment       Pairing the elements of a GAlignments object
findOverlaps-methods    Finding overlapping genomic alignments
findSpliceOverlaps-methods
                        Classify ranges (reads) as compatible with
                        existing genomic annotations or as having novel
                        splice events
intra-range-methods     Intra range transformations of a GAlignments or
                        GAlignmentsList object
junctions-methods       Extract junctions from genomic alignments
map,GenomicRanges,GAlignments-method
                        Mapping ranges between sequences
pileLettersAt           Pile the letters of a set of aligned reads on
                        top of a set of individual genomic positions
readGAlignments         Reading genomic alignments from a file
sequenceLayer           Lay read sequences alongside the reference
                        space, using their CIGARs
setops-methods          Set operations on GAlignments objects
stackStringsFromBam     Stack the read sequences stored in a BAM file
                        on a region of interest
summarizeOverlaps-methods
                        Perform overlap queries between reads and
                        genomic features