### From an NCBI "agp" file (for chrY in hs b36v3):
###   file1 <- system.file("extdata", "hs_b36v3_chrY.agp", package="IRanges")
###   mask1 <- read.agpMask(file1, seqname="chrY", mask.width=length(Hsapiens$chrY))
### From an UCSC "gap" file (for chrY in hg18):
###   file2 <- system.file("extdata", "chrY_gap.txt", package="IRanges")
###   mask2 <- read.gapMask(file2, seqname="chrY", mask.width=length(Hsapiens$chrY))
### From an UCSC "lift" file (for hg18):
###   file3 <- system.file("extdata", "hg18liftAll.lft", package="IRanges")
###   mask3 <- read.liftMask(file3, seqname="chr1")
### From a RepeatMasker .out file (for chrM in ce2):
###   file4 <- system.file("extdata", "ce2chrM.fa.out", package="IRanges")
###   mask4 <- read.rmMask(file4, seqname="chrM", mask.width=length(Celegans$chrM))
### From a Tandem Repeats Finder .bed file (for chrM in ce2):
###   file5 <- system.file("extdata", "ce2chrM.bed", package="IRanges")
###   mask5 <- read.trfMask(file5, seqname="chrM", mask.width=length(Celegans$chrM))
" distinct seqnames found in this file: "
"  'mask.width' argument to specify the width of the empty mask to\n"
"  return (i.e. the length of the sequence this mask will be put on)."
### read.agpMask() and read.gapMask() extract the AGAPS mask from an NCBI
### "agp" file or a UCSC "gap" file, respectively.
## UCSC "gap" files generally have the 9 columns below except for some
## organisms like Rhesus that have only 8 columns (no 'bin' column).
"unable to guess the column names in \"gap\" file '"
"read.Mask internal error: please report"
"'mask.width' must be a single integer or 'NA'"
"'gap.types' must be 'NULL' or a character vector "
"gap file contains gaps with a part_type that is not N"
"gap types found in this file for sequence \""
"cannot use the gap types when some gaps are adjacent or overlap"
## Don't use new2(): the validity of the new mask needs to be checked!
### read.liftMask() extracts the AGAPS mask from a UCSC "lift" file.
"broken \"lift\" file: contains different lengths "
"when supplied, 'mask.width' must match the length found "
"some contigs are adjacent or overlapping"
### read.rmMask() extracts the RM mask from a RepeatMasker .out file.
### See http://www.repeatmasker.org/webrepeatmaskerhelp.html for a
### description of the RepeatMasker output format.
"cannot use the repeat IDs when some repeats are adjacent or overlap"
### read.trfMask() extracts the TRF mask from a Tandem Repeats Finder .bed