Modified for RSEM by Bo Li: Let the query name stops whenever encounters a space

Returns the @c t parameter of the distribution. */

* 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 */

* Tokenises the search path splitting on colons (unix) or semicolons * (windows). * We also explicitly add a "./" to the end of the search path *

update read information vector etc

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

creates index data (in-memory) from current reader data

creates index data (in-memory) from current reader data

closes BGZF file

closes the alignment archive

closes BGZF file

closes the alignment archive

index operations

index operations

returns supported file extension

returns supported file extension

get "NM" tag data - originally contributed by Aaron Quinlan stores data in 'editDistance', returns success/fail

get "NM" tag data - originally contributed by Aaron Quinlan stores data in 'editDistance', returns success/fail

access alignment data

access alignment data

get next alignment among all files without parsing character data from alignments

get next alignment among all files without parsing character data from alignments

loads existing data from file into memory

loads existing data from file into memory

opens the BGZF file for reading (mode is either "rb" for reading, or "wb" for writing)

opens the BGZF file for reading (mode is either "rb" for reading, or "wb" for writing)

Advances in the bit stream by "popping" a single symbol with range start "start" and frequency "freq". All frequencies are assumed to sum to "1 << sca

Advances in the bit stream by "popping" a single symbol with range start "start" and frequency "freq". All frequencies are assumed to sum to "1 << sca

Renormalize the encoder. Internal function.

swaps endianness of 16-bit value 'in place'

swaps endianness of 16-bit value 'in place'

! @function @abstract const char* hash function @param s Pointer to a null terminated string @return The hash value */

* _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 */

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