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Fix cram_dependent_data_series when FN is used. #1314

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Fix cram_dependent_data_series when FN is used. #1314

wants to merge 1 commit into from

Commits on Aug 5, 2021

  1. Fix cram_dependent_data_series when FN is used. 

    If we get into the primary loop of cram_decode_seq, iterating over
feature (count FN) then we have unguarded code that always checks for
sequence overlapping the reference.  To do this, seq_pos must be set.
Some data series we know how seq_pos is adjusted irrespective of
whether we decode, eg BS is always +1, but others are strings and the
only way we know how to update seq_pos is to decode them.

Hence added FN as having a dependency on SC, IN and BB.

Fixes samtools/samtools#1475
    @jkbonfield
    jkbonfield committed Aug 5, 2021
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