* Looks for a specific key in a single sam header line. * If prev is non-NULL it also fills this out with the previous tag, to * permit use in key r

Adapted from kent source "binKeeperFind" */

Returns the current cumulative frequency (map it to a symbol yourself!)

s MUST BE returned by bam_aux_get()

* Absolute htell in this compressed file. * * Do not confuse with the external bgzf_tell macro which returns the virtual * offset. */

* This processes one or more 64-byte data blocks, but does NOT update * the bit counters. There are no alignment requirements. */

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

* Returns 1 if we hit an EOF while reading. */

* Sets options on the cram_fd. See CRAM_OPT_* definitions in cram_structs.h. * Use this immediately after opening. * * Returns 0 on success *

Store a float value in little-endian byte order @param val The value to store * @param buf Where to store it (may be unaligned) */

Flushes the write buffer, fp->[buffer,begin), out through the backend returning 0 on success or negative if an error occurred. */

tokenize into a list of strings.

Return the stream's error indicator @return Non-zero (in fact, an _errno_ value) if an error has occurred. This would be called `herror()` and retur

* As above but optional non-block flag. * * nonblock 0 => block if input queue is full * nonblock +1 => don't block if input queue is full, but do

* Pulls the next item off the process result queue. The caller should free * it (and any internals as appropriate) after use. This doesn't wait for

Store a uint32_t value in little-endian byte order @param val The value to store * @param buf Where to store it (may be unaligned) */

* Decodes a 32-bit little endian value from fd and stores in val. * * Returns the number of bytes read on success * -1 on failure */

returns TRUE if the file has a GZIP header. Should only be run on regular files. */

The <ctype.h> functions operate on ints such as are returned by fgetc(), i.e., characters represented as unsigned-char-valued ints, or EOF. To operate

Destroy a bit set.

* Destroy the hash structure, but not the keys */

* Set a new key,value pair. On success returns the bin index, on * error -1 is returned. Note that the key must contnue to exist * throughout the

* Destroys an mFILE structure but does not flush or close it */

* Creates a pool. * Pool allocations are approx minimum of 1024*dsize or PSIZE. * (Assumes we're not trying to use pools for >= 2Gb or more) */

Refills the read buffer from the backend (once, so may only partially fill the buffer), returning the number of additional characters read (whic

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

* 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

! Deallocates all storage used by a SAM_hdr struct. * * This also decrements the header reference count. If after decrementing * it is still non-ze

* 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

are the any intervals left in the file?

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