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Revert defn of CRAM container size to be sum of block sizes (PR#731) #731

Merged
merged 1 commit into from
Aug 6, 2024
Merged

Revert defn of CRAM container size to be sum of block sizes (PR#731) #731

merged 1 commit into from
Aug 6, 2024

Commits on Sep 27, 2023

  1. Revert defn of CRAM container size to be sum of block sizes (PR#731) 

    This was added as clarification in samtools#398 after discussion in samtools#396, but
this was in error.  In our attempts to clarify and nail down these
corner cases, we failed to recall that the SAM header is permitted to
be padded out by non-block allocated space.

History on this decision dates back to 2013 and is show in Samtools
issue samtools/samtools#1852.

There are good reasons for changing away from the decision of padding
via a second block, as changing block sizes can also change block
structure size (if we're using a generic shared piece of code, due to
ITF8 being a variable length integer), and this in turn makes it
cumbersome to handle every possible change in SAM header size.  It is
far easier and simpler to just have unallocated space after the block
and before the end of the container.  This is how htslib works since
CRAM 3.0 and I believe how CRAMtools.jar works.

Fixes samtools/samtools#1852.
    @jkbonfield
    jkbonfield committed Sep 27, 2023
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