* Creates a new container, specifying the maximum number of slices * and records permitted. * * Returns cram_container ptr on success * NU

get filtered count

find the n-th bit set in a 8-bit mask (n in [1,8])

get a context

========================================================================= */

Fetch data and put it in the output buffer. Assumes state->x.have is 0. Data is either copied from the input file or decompressed from the input

Use read() to load a buffer -- return -1 on error, otherwise 0. Read from state->fd, and update state->eof, state->err, and state->msg as appropri

Skip len uncompressed bytes of output. Return -1 on error, 0 on success. */

returns true if the stream is ready to read from

* Encodes and writes a single integer in ITF-8 format. * Returns 0 on success * -1 on failure */

log\binom{n}{k}

string length

granularity of the maximum grid size

* Flushes an mFILE. If this is a real open of a file in write mode then * mFILE->fp will be set. We then write out any new data in mFILE since the *

get the compress level from the mode string

bogus implementation of a function to check if an option is a function

@details Identical to std::priority_queue pop(). @see @a pop_maximum

raw output queue

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

* Indexes references by the order they appear in a BAM file. This may not * necessarily be the same order they appear in the fasta reference file. *

reserve enough storage for a given number of reads and bps

resize the arena \param size size of the array (i.e. number of vectors) \param arena size of the memory arena \param do_alloc a flag to ind

* Looks up a read-group by name and returns a pointer to the start of the * associated tag list. * * Returns NULL on failure */

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