Provide extra CRAM container manipulations and index queries.
Added to support extra functionality to samtools cat.
Some internal cram functions are no longer static as they're called
from cram_external.c, but they don't have HTSLIB_EXPORT and aren't
an official part of the API.
These are cram_to_bam, cram_next_slice
New public CRAM APIs:
These facilitate manipulation at the container level, both seeking to specific byte offsets, but also being able to specify containers as the n^th container listed in the index.
cram_container_get_coords returns refid, start and span fields from the opaque cram_container struct.
cram_filter_container copies a container but applies region based filtering, as already specified in the cram_fd with a range request. (Note we currently also provide cram_copy_slice, but may want to add a cram_copy_container for consistency.)
cram_index_extents queries an index to return byte offsets of the first and last container overlapping a specified region.
cram_num_containers_between queries an index to report the number of indexed containers and their container numbers (starting at 0 for the first) covering a range.
cram_num_containers is a simplified cram_num_containers_between doing only the counting operation and on the entire file.
cram_container_num2offset returns the byte offset for the n^th container. cram_container_offset2num does the reverse.
A new cram_skip_container function, which is currently internal only but may potentially have use externally in the future. It's used by cram_filter_container when it detects it'll filter out everything.
cram_index_query now copes with HTS_IDX_NOCOOR (-2) and maps it over to refid -1.
Also improved cram_index_query so it works on region HTS_IDX_NOCOOR too, rather than requiring a remapping to CRAM's -1.
Provide extra CRAM container manipulations and index queries.
Added to support extra functionality to
samtools cat.Some internal cram functions are no longer static as they're called from cram_external.c, but they don't have HTSLIB_EXPORT and aren't an official part of the API. These are cram_to_bam, cram_next_slice
New public CRAM APIs: These facilitate manipulation at the container level, both seeking to specific byte offsets, but also being able to specify containers as the n^th container listed in the index.
cram_container_get_coords returns refid, start and span fields from the opaque cram_container struct.
cram_filter_container copies a container but applies region based filtering, as already specified in the cram_fd with a range request. (Note we currently also provide cram_copy_slice, but may want to add a cram_copy_container for consistency.)
cram_index_extents queries an index to return byte offsets of the first and last container overlapping a specified region.
cram_num_containers_between queries an index to report the number of indexed containers and their container numbers (starting at 0 for the first) covering a range.
cram_num_containers is a simplified cram_num_containers_between doing only the counting operation and on the entire file.
cram_container_num2offset returns the byte offset for the n^th container. cram_container_offset2num does the reverse.
A new cram_skip_container function, which is currently internal only but may potentially have use externally in the future. It's used by cram_filter_container when it detects it'll filter out everything.
cram_index_query now copes with HTS_IDX_NOCOOR (-2) and maps it over to refid -1.
Also improved cram_index_query so it works on region HTS_IDX_NOCOOR too, rather than requiring a remapping to CRAM's -1.