* Returns 0 on success and -1 when the key is not present. On success, * *value is set, unless NULL is passed. */

string length

Returns the number of bits set in val; it the highest bit used */

factory method to open a read file, tries to detect file type based on file name

process a batch of BWT symbols

* Generates refs_t entries based on @SQ lines in the header. * Returns 0 on success * -1 on failure */

a client method to release the latest batch

* Returns the first header item matching 'type'. If ID is non-NULL it checks * for the tag ID: and compares against the specified ID. * * Returns N

Insertionsort for small size groups */

Multikey introsort for medium size groups. */

* Can store up to 24-bits worth of data encoded in an integer value * Possibly we'd want to have a less optimal store_bits function when dealing * w

ichr,ifrom,ito are 0-based; returns -1 on error, 0 if the line is a comment line, 1 on success

Prepares next pileup position in bam records collected by bam_plp_auto -> user func -> bam_plp_push. Returns pointer to the piled records if next posi

return the number of bits per symbol for a given alphabet

build a set of buckets pointing to the lower/upper bounds of a sequence of keys

=========================================================================== * Construct one Huffman tree and assigns the code bit strings and lengths

=========================================================================== * Check that the match at match_start is indeed a match. */

=========================================================================== If the default memLevel or windowBits for deflateInit() is changed, t

* Decodes a CRAM block compression header. * Returns header ptr on success * NULL on failure */

* Decode an entire slice from container blocks. Fills out s->crecs[] array. * Returns 0 on success * -1 on failure */

* Read the next cram record and convert it to a bam_seq_t struct. * * Returns 0 on success * -1 on EOF or failure (check fd->err) */