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/*
* The MIT License
*
* Author: Pierre Lindenbaum PhD @yokofakun
* Institut du Thorax - Nantes - France
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package htsjdk.samtools;
import java.util.HashSet;
import java.util.Set;
/**
* SAM flags as enum, to be used in GUI, menu, etc...
*/
public enum SAMFlag {
READ_PAIRED( 0x1, "Template having multiple segments in sequencing"),
PROPER_PAIR( 0x2, "Each segment properly aligned according to the aligner"),
READ_UNMAPPED( 0x4, "Segment unmapped"),
MATE_UNMAPPED( 0x8, "Next segment in the template unmapped"),
READ_REVERSE_STRAND( 0x10, "SEQ being reverse complemented"),
MATE_REVERSE_STRAND( 0x20, "SEQ of the next segment in the template being reverse complemented"),
FIRST_OF_PAIR( 0x40, "The first segment in the template"),
SECOND_OF_PAIR( 0x80, "The last segment in the template"),
SECONDARY_ALIGNMENT( 0x100, "Secondary alignment"),
/** @deprecated use {@link #SECONDARY_ALIGNMENT} instead. */
@Deprecated
NOT_PRIMARY_ALIGNMENT( 0x100, "Secondary alignment"),
READ_FAILS_VENDOR_QUALITY_CHECK(0x200, "Not passing quality controls"),
DUPLICATE_READ( 0x400, "PCR or optical duplicate"),
SUPPLEMENTARY_ALIGNMENT( 0x800, "Supplementary alignment")
;
/* visible for the package, to be used by SAMRecord */
final int flag;
private final String description;
SAMFlag(int flag, String description) {
this.flag = flag;
this.description = description;
}
/** @return this flag as an int */
public int intValue() {
return flag;
}
/** @return a human label for this SAMFlag */
public String getLabel() {
return name().toLowerCase().replace('_', ' ');
}
/** @return a human description for this SAMFlag */
public String getDescription() {
return this.description;
}
/** @return the SAMFlag for the value 'flag' or null if it was not found */
public static SAMFlag valueOf(int flag) {
for (SAMFlag f : values()) {
if (flag == f.flag)
return f;
}
return null;
}
/** @return find SAMFlag the flag by name, or null if it was not found */
public static SAMFlag findByName(String flag)
{
for (SAMFlag f : values()) {
if (f.name().equals(flag))
return f;
}
return null;
}
/** @returns true if the bit for is set for flag */
public boolean isSet(int flag) {
return (this.flag & flag) != 0;
}
/** @returns true if the bit for is not set for flag */
public boolean isUnset(int flag) {
return !isSet(flag);
}
/** @returns the java.util.Set of SAMFlag for 'flag' */
public static Set getFlags(int flag) {
Set set = new HashSet();
for (SAMFlag f : values()) {
if (f.isSet(flag))
set.add(f);
}
return set;
}
}
