hts_fmt_option

Mostly CRAM only, but this could also include other format options

Values

ValueMeaning
CRAM_OPT_DECODE_MD
CRAM_OPT_PREFIX
CRAM_OPT_VERBOSITY

obsolete, use hts_set_log_level() instead

CRAM_OPT_SEQS_PER_SLICE
CRAM_OPT_SLICES_PER_CONTAINER
CRAM_OPT_RANGE
CRAM_OPT_VERSION

rename to cram_version?

CRAM_OPT_EMBED_REF
CRAM_OPT_IGNORE_MD5
CRAM_OPT_REFERENCE
CRAM_OPT_MULTI_SEQ_PER_SLICE
CRAM_OPT_NO_REF
CRAM_OPT_USE_BZIP2
CRAM_OPT_SHARED_REF
CRAM_OPT_NTHREADS

deprecated, use HTS_OPT_NTHREADS

CRAM_OPT_THREAD_POOL

make general

CRAM_OPT_USE_LZMA
CRAM_OPT_USE_RANS
CRAM_OPT_REQUIRED_FIELDS
CRAM_OPT_LOSSY_NAMES
CRAM_OPT_BASES_PER_SLICE
CRAM_OPT_STORE_MD
CRAM_OPT_STORE_NM
HTS_OPT_COMPRESSION_LEVEL100
HTS_OPT_NTHREADS
HTS_OPT_THREAD_POOL
HTS_OPT_CACHE_SIZE
HTS_OPT_BLOCK_SIZE

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