SAMReader

Encapsulates a SAM/BAM file.

Implements InputRange interface using htslib calls. If indexed, Random-access query via multidimensional slicing.

Constructors

this this(T f, int extra_threads): Create a representation of SAM/BAM/CRAM file from given filename or File

all_records AllRecordsRange all_records(): Return an InputRange representing all recods in the SAM/BAM/CRAM
n_targets int n_targets(): number of reference sequences; from bam_hdr_t
opIndex auto opIndex(string q): bam["chr1:1-2"]
opIndex auto opIndex(string tid, int[2] pos): bam["chr1", 1..2]
opIndex auto opIndex(string tid, int pos): bam["chr1", 1]
opIndex auto opIndex(string tid, int pos1, int pos2)
opIndex auto opIndex(int tid, int[2] pos): Integer-based chr below bam[0, 1..2]
opIndex auto opIndex(int tid, int pos): bam[0, 1]
opIndex auto opIndex(int tid, int pos1, int pos2): bam[0, 1, 2]
opSlice int[2] opSlice(int start, int end): support bam["chr1", 1..2 ]
query auto query(string chrom, long start, long end): Query a region and return matching alignments as an InputRange Query by chr, start, end
query auto query(string q): Query by string chr:start-end
query auto query(int tid, long start, long end): Query by contig id, start, end
query auto query(string[] regions): Query by ["chr1:1-2","chr1:1000-1001"]
target_id int target_id(string name): reference contig name to integer id Calls int bam_name2id(bam_hdr_t *h, const char *_ref);
target_len uint target_len(int target): length of specific reference sequence (by number)
target_lens uint[] target_lens(): lengths of the reference sequences
target_names string[] target_names(): names of the reference sequences

AllRecordsRange struct AllRecordsRange: Iterate through all records in the SAM/BAM/CRAM
RecordRange struct RecordRange: Iterate over records falling within a queried region (TODO: itr_multi_query)
RecordRangeMulti struct RecordRangeMulti: Iterate over records falling within queried regions using a RegionList
RegionList struct RegionList: List of regions based on sam/bam