Expose the set of tags to reverse and reverse complement as parameters. #673
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| reverseComplement(rec, TAGS_TO_REVERSE_COMPLEMENT, TAGS_TO_REVERSE); | ||
| } | ||
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| public static void reverseComplement(final SAMRecord rec, Collection<String> tagsToRevcomp, Collection<String> tagsToReverse) { |
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Comments made. @nh13 should feel free to comment himself (as the assigned reviewer) or just assign to me. |
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@tfenne 👍 me but please respond to @eitanbanks comments. |
| SAMTagUtil.getSingleton().OQ | ||
| }; | ||
| private static List<String> TAGS_TO_REVERSE_COMPLEMENT = Arrays.asList(SAMTag.E2.name(), SAMTag.SQ.name()); | ||
| private static List<String> TAGS_TO_REVERSE = Arrays.asList(SAMTag.OQ.name(), SAMTag.U2.name()); | ||
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| /** | ||
| * Reverse-complement all known sequence and base quality attributes of the SAMRecord. |
tfenne
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Looks like just the |
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Description
Expose the set of tags to reverse and reverse complement as parameters, so that reads can be reverse complemented and all tags that are one-value-per-base in the read can be kept in sync.
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