Renable changing CRAM compression level via hts_set_opt.#1203
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daviesrob merged 1 commit intosamtools:developfrom Jan 18, 2021
Merged
Renable changing CRAM compression level via hts_set_opt.#1203daviesrob merged 1 commit intosamtools:developfrom
daviesrob merged 1 commit intosamtools:developfrom
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This bug was introduced during samtools#1181 where the additional HTS_OPT_FILTER meant the automatic fall-through from HTS_OPT_COMPRESSION_LEVEL no longer applied. I decided against continuing the previous obscurity of moving HTS_OPT_COMPRESSION_LEVEL to the end of the switch and having no return (thus falling into the cram_set_voption call), instead favouring an explicit call. An example command that demonstrated the problem was: samtools view -O cram,level=1 in.bam -o out.cram
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This bug was introduced during #1181 where the additional
HTS_OPT_FILTER meant the automatic fall-through from
HTS_OPT_COMPRESSION_LEVEL no longer applied.
I decided against continuing the previous obscurity of moving
HTS_OPT_COMPRESSION_LEVEL to the end of the switch and having no
return (thus falling into the cram_set_voption call), instead
favouring an explicit call.
An example command that demonstrated the problem was: