Updating SAMTag and SAMTagUtils #1208
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lbergelson
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magicDGS
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Oct 28, 2018
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Another approach would be to move the binary tag directly into the SAMTag enum. e.g.
public enum SAMTag {
AM,
...
U2,
UQ;
public final short binaryTag;
SAMTag() {
binaryTag = makeBinaryTag(this.name());
}
}
You could also move makeStringTag(), makeBinaryTag() into SAMTag, and delete SAMTagUtil, or deprecate it and forward the methods and fields for now.
| /** | ||
| * This constructor is public despite being a utility class for backwards compatibility reasons. | ||
| */ | ||
| public SAMTagUtil(){} |
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Shouldn't this be deprecated too?
| } else { | ||
| encodedTag = tagCodec.encode(tagUtil.makeStringTag(attribute.tag), attribute.value); | ||
| encodedTag = tagCodec.encode(SAMTagUtil.makeStringTag(attribute.tag), attribute.value); |
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Now that tagUtil is unused it should be deleted.
|
@pshapiro4broad @magicDGS Thanks for the reviews. |
Codecov Report
@@ Coverage Diff @@
## master #1208 +/- ##
===============================================
+ Coverage 68.978% 69.037% +0.058%
- Complexity 8073 8092 +19
===============================================
Files 539 539
Lines 32587 32658 +71
Branches 5510 5513 +3
===============================================
+ Hits 22478 22546 +68
- Misses 7903 7905 +2
- Partials 2206 2207 +1
|
* adding new tags that were introduced in the spec * Cellular barcode tags s CB, CR, and CY added * Unique mollecular identifier tags BZ, MI, OX, QX, and RX added. * deprecating tag constants that are for backward compatibility only
* Making methods in SAMTagUtil final and deprecating the use of the getSingleton() method. * This is a breaking change to SAMTagUtil, it will break any subclasses, all other uses should be compatible
Co-Authored-By: lbergelson <[email protected]>
Co-Authored-By: lbergelson <[email protected]>
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Description
This PR does several things: