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Updating SAMTag and SAMTagUtils #1208

Merged
merged 7 commits into from
Nov 14, 2018
Merged

Updating SAMTag and SAMTagUtils #1208

merged 7 commits into from
Nov 14, 2018

Commits on Nov 14, 2018

  1. Update SAMTag to include new tags 

    * 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
    @lbergelson
    lbergelson committed Nov 14, 2018
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  2. Modernizing SAMTag and SAMTagUtil 

    * 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
    @lbergelson
    lbergelson committed Nov 14, 2018
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  3. Update src/main/java/htsjdk/samtools/SAMTag.java 

    Co-Authored-By: lbergelson <[email protected]>
    @magicDGS @lbergelson
    magicDGS and lbergelson committed Nov 14, 2018
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  4. Update SAMTagUtil.java

    @lbergelson
    lbergelson committed Nov 14, 2018
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  5. Update src/main/java/htsjdk/samtools/SAMTagUtil.java 

    Co-Authored-By: lbergelson <[email protected]>
    @pshapiro4broad @lbergelson
    pshapiro4broad and lbergelson committed Nov 14, 2018
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  6. more fixup

    @lbergelson
    lbergelson committed Nov 14, 2018
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  7. resolving circular classloading issue and removing uses of constants … 

    …in SamTagUtil
    @lbergelson
    lbergelson committed Nov 14, 2018
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