sp <- SolexaPath(system.file("extdata", package="ShortRead"))
filter <- chipseqFilter()
aln <- readAligned(sp, "s_2_export.txt", filter=filter)
## allow mapping to the same location (but only if sequence is different)
filter <- chipseqFilter(uniqueness = "sequence")
aln <- readAligned(sp, "s_2_export.txt", filter=filter)
## allow sex chromosomes
filter <- chipseqFilter(exclude = "[M_]")
aln <- readAligned(sp, "s_2_export.txt", filter=filter)
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