setup the input thread

setup the input thread

Sorts suffixes of type B*. */

D&C based merge. */

Substring sort */

return the base stream

* Destroys a thread pool. If 'kill' is true the threads are terminated now, * otherwise they are joined into the main thread so they will finish thei

* Adds an item to the work pool. * * FIXME: Maybe return 1,0,-1 and distinguish between job dispathed vs * result returned. Ie rather than blocking

* Flushes the pool, but doesn't exit. This simply drains the queue and * ensures all worker threads have finished their current task. * * Returns 0

* Creates a worker pool of length qsize with tsize worker threads. * * Returns pool pointer on success; * NULL on failure */

Core of t_pool_next_result() */

Deallocates memory for a results queue */

td_object::td_object(FILE* output, const uint32 value, ...) : m_output( output ) { va_list args; va_start(args, value); char name[1024

min score function

@details Identical to std::priority_queue top(). @see @a maximum

Update the window with the last wsize (normally 32K) bytes written before returning. If window does not exist yet, create it. This is only called

returns the width of the tree at the level of node i

---------------------------------------------------------------------- * zlib compression code - from Gap5's tg_iface_g.c * They're static here as t

closes the alignment archive

compresses the current block

get "NM" tag data - contributed by Aaron Quinlan

access alignment data

Returns true if alignment is first mate on read

LaunchBox properties.

for private usage. Use free standing get_deleter() instead

* _reader_fill_buffer() - buffers all records with the same coordinate */

* _reader_match_alleles() - from multiple buffered lines selects the one which * corresponds best to the template line. The logic is controlled by

* _readers_shift_buffer() - removes the first line and all subsequent lines with the same position */

* _readers_next_region() - jumps to next region if necessary * Returns 0 on success or -1 when there are no more regions left */

=========================================================================== * Send one empty static block to give enough lookahead for inflate. * Th

=========================================================================== * Initialize the tree data structures for a new zlib stream. */

p,q is the start and the end of the FORMAT field

add a client

return the amount of used device memory

--------------------------------------------------------------------------- * Samtools compatibility portion */