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Remove limit on returned size from fai_retrieve() #1446

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merged 1 commit into from
Jun 8, 2022

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This was probably a left-over from the transition to 64-bit positions in HTSlib. Having the limit in fai_retrieve() caused
very long references to be truncated even though programs like samtools faidx should be able to support them (see issue samtools/samtools#1660 - samtools faidx fails to retrieve large scaffolds).

The limit is useful for legacy faidx interfaces that return the size in an int *, so tests for sizes over INT_MAX have been applied to them.

This was probably a left-over from the transition to 64-bit
positions in HTSlib.  Having the limit in fai_retrieve() caused
very long references to be truncated even though programs like
`samtools faidx` should be able to support them (see issue
samtools/samtools#1660 - samtools faidx fails to retrieve large
scaffolds).

The limit is useful for legacy faidx interfaces that return
the size in an `int *`, so tests for sizes over INT_MAX
have been applied to them.
@whitwham whitwham merged commit 2978708 into samtools:develop Jun 8, 2022
@daviesrob daviesrob deleted the fai_retrieve_limit branch June 8, 2022 12:01
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