$ flex input.l && gcc -O3 lex.yy.c && curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chr22.fa.gz" | gunzip -c | ./a.out
chr22 0 16050000
chr22 16697850 16847850
chr22 19178139 19178140
chr22 19178159 19178160
chr22 19178161 19178164
chr22 19178165 19178167
chr22 19178168 19178169
chr22 19178263 19178264
chr22 19178267 19178268
chr22 19178273 19178274
chr22 19178283 19178284
chr22 19178310 19178311
chr22 19178314 19178315
chr22 19179518 19179519
chr22 19193925 19193926
chr22 19200634 19200635
chr22 19200640 19200641
chr22 19205396 19205397
chr22 19205400 19205401
chr22 19205448 19205449
chr22 20509431 20609431
chr22 50364777 50414777
Is there a R package to identify long stretches of gaps (Ns) in human genome (hg19)?
Are you looking for hard-masked repeat regions or just N's at ends of chromosomes?
I am looking for regions were it is obvious to find gaps (N's) in hg19, I am not looking into hard masked repeat regions.