As int32_decoded/encode, but from/to blocks instead of cram_fd */

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

complementary error function * \frac{2}{\sqrt{\pi}} \int_x^{\infty} e^{-t^2} dt * AS66, 2nd algorithm, http://lib.stat.cmu.edu/apstat/66 */

* Returns 1 if key exists or 0 if not */

log\binom{n}{k}

* 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 *

Returns the "n" parameter of the distribution. */

Returns: the distribution parameter @c p */

Returns the parameters of the distribution. */

Takes the command line options and turns them into something we can understand

* 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) */

* Returns a vector containing the probabilities of each * value of the distribution. For example, given * * @code * discrete_dist

----------------------------------------------------------------------------- * Simple interface to the order-0 vs order-1 encoders and decoders. */

* Frees/unmaps a reference sequence and associated file handles. */

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. *

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

* sam_hdr_add with a va_list interface. * * Note: this function invokes va_arg at least once, making the value * of ap indeterminate after the retu

arr should be cumulative! interval : [,) random number should be in [0, arr[len - 1]) If by chance arr[len - 1] == 0.0, one possibility is to sample u

This function does not work with Windows due to the lack of * getaddrinfo() in winsock. It is addapted from an example in "Beej's * Guide to Network

This function tests if the file handler is ready for reading (or * writing if is_read==0). */

* Pulls a result off the head of the result queue. Caller should * free it (and any internals as appropriate) after use. This doesn't * wait for a r

* Initialises a results queue. * * Results queue pointer on success; * NULL on failure */

* A wrapper for either fputs or gzputs depending on what has been * opened. */

constructor

constructor

get next alignment among all files

get next alignment among all files

returns whether reference has alignments or no

returns whether reference has alignments or no

return true if FILE* is open

return true if FILE* is open

Initialize a decoder symbol to start "start" and frequency "freq"

Initializes an encoder symbol to start "start" and frequency "freq"

swaps endianness of 'next 2 bytes' in a char buffer (in-place)

swaps endianness of 'next 2 bytes' in a char buffer (in-place)

swaps endianness of 'next 8 bytes' in a char buffer (in-place)

swaps endianness of 'next 8 bytes' in a char buffer (in-place)

regularized lower incomplete gamma function, by series expansion

regularized upper incomplete gamma function, by continued fraction

File name or a list of genomic locations. If file name, NULL is returned.

Returns the "a" parameter of the distribution. */

Returns the "a" parameter of the distribution. */

Returns the @c a parameter of the distribution */