+ "If given, must be indexed, e.g. with `samtools faidx ref.fa`");
parser.addArgument("--exec", "-x")
.type(String.class)
.setDefault("")
.help("Commands to be executed at the prompt. Must be a single string. E.g. 'goto chr1 && next && seqRegex ACTG'");
<BUG>parser.addArgument("--maxReadsStack", "-M")
.type(Integer.class)
.setDefault(2000)
.help("Maximum number of reads to accumulate before printing. If more than this many reads map to the window\n"
+ "randomy select them");</BUG>
parser.addArgument("--noFormat", "-nf")

+ "If given, must be indexed, e.g. with `samtools faidx ref.fa`");
parser.addArgument("--exec", "-x")
.type(String.class)
.setDefault("")
.help("Commands to be executed at the prompt. Must be a single string. E.g. 'goto chr1 && next && seqRegex ACTG'");
parser.addArgument("--noFormat", "-nf")
