public boolean bedType(File bedFile) {
stranded = false;
scored = false;
named = false;
bed12 = false;
boolean bedLineFound = false;
try {
// read through first 10000 lines
// chrom start stop name score strand ....
// 0 1 2 3 4 5
BufferedReader in = IO.fetchBufferedReader(bedFile);
String[] tokens;
String line;
int counter = 0;
while ((line = in.readLine()) != null) {
if (counter++ > 10000) break;
// bed line?
if (bedLine.matcher(line).matches() == false) continue;
bedLineFound = true;
// split on tab
tokens = tab.split(line);
// bed12?
if (tokens.length == 12) {
bed12 = true;
break;
}
if (tokens.length > 3) {
// named?
if (badName.matcher(tokens[3]).matches() == false) named = true;
if (tokens.length > 4) {
// scored?
if (tokens[4].equals("0") == false) scored = true;
if (tokens.length > 5) {
// stranded?
if (tokens[5].equals(".") == false) stranded = true;
}
}
}
}
in.close();
} catch (Exception e) {
System.err.println("\nProblem parsing bed type.\n");
e.printStackTrace();
bedLineFound = false;
}
return bedLineFound;
}
