sample iterations

setup the number of input reads

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). */

Binary partition for substrings. */

Store an array of hits into a SeedHitDequeArray

* 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 */

return whether the file is valid

return a device-side view

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

Size is in units of T, not bytes.

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.

=========================================================================== * Flush the bits in the bit buffer to pending output (leaves at most 7 bi

=========================================================================== * Send a stored block */

acquire element i

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

allocate some storage for the deque bound to a given read

return the amount of used device memory

return the amount of used device memory

Copies all fields except IDX.

=========================================================================== * Flush the bit buffer, keeping at most 7 bits in it. */

=========================================================================== * Reverse the first len bits of a code, using straightforward code (a fas

=========================================================================== * Flush the bit buffer and align the output on a byte boundary */

extract the bwt of the given block

convert an ASCII RNA representation to its 2-bit symbol

* cigar_iref2iseq_set() - find the first CMATCH setting the ref and the read index * cigar_iref2iseq_next() - get the next CMATCH base * @cigar:

reset the list

clear the syncblocks, useful if one wants to reuse it across differently sized kernel launches.