* bcf_hdr_name2id() - Translates sequence names (chromosomes) into numeric ID * bcf_hdr_id2name() - Translates numeric ID to sequence name

returns: 1 when hdr needs to be synced, 0 otherwise

signals that a batch is to begin

=========================================================================== * Construct the Huffman tree for the bit lengths and return the index in

convert an ASCII character to a Protein symbol

Returns: 0 on success (BGZF header); -1 on non-BGZF GZIP header; -2 on error

clear internal timers

clear internal timers

Removes duplicate records from the buffer. The meaning of "duplicate" is controlled by the $collapse variable, which can cause that from multiple

scatter flags/slots/indices to the position specified by keys (-1) only if the given stencil is true

compress all of input into the current position of the output buffer note that this assumes output has enough space!

=========================================================================== Compresses the source buffer into the destination buffer. The level

compute the CIGAR alignment position given the alignment base and the sink offset

Constructs the burrows-wheeler transformed string directly by using the sorted order of type B* suffixes. */

Constructs the suffix array by using the sorted order of type B* suffixes. */

construct a debruijn assembly graph with the given kmer length

=========================================================================== * Copy a stored block, storing first the length and its * one's compleme

count the number of suffixes falling in each bucket, where the buckets are defined by the first n_bits of the suffix

* Closes a CRAM file. * Returns 0 on success * -1 on failure */

* Decodes the Tag Dictionary record in the preservation map * Updates the cram compression header. * * Returns number of bytes decoded on success

* Internal part of cram_decode_slice(). * Generates the sequence, quality and cigar components. */

* Decodes a CRAM (un)mapped slice header block. * Returns slice header ptr on success * NULL on failure */