// Copyright (C) 2011-2012 CRS4.
//
// This file is part of Seal.
//
// Seal is free software: you can redistribute it and/or modify it
// under the terms of the GNU General Public License as published by the Free
// Software Foundation, either version 3 of the License, or (at your option)
// any later version.
//
// Seal is distributed in the hope that it will be useful, but
// WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
// or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
// for more details.
//
// You should have received a copy of the GNU General Public License along
// with Seal. If not, see <http://www.gnu.org/licenses/>.
package it.crs4.seal.common;
public enum AlignFlags {
Paired(1),
ProperlyPaired(2),
Unmapped(4),
MateUnmapped(8),
OnReverse(16),
MateOnReverse(32),
Read1(64),
Read2(128),
SecondaryAlignment(256),
FailedQC(0x200),
Duplicate(0x400);
private final int bit;
private AlignFlags(int bit) {
this.bit = bit;
}
public boolean is(int flag) {
return (bit & flag) != 0;
}
public boolean isNot(int flag) {
return (bit & flag) == 0;
}
/**
* Set this flag's bit in bitset.
*/
public int set(int bitset) {
return bitset | bit;
}
/**
* Clear this flag's bit from bitset.
*/
public int clear(int bitset) {
return bitset & ~bit;
}
}