* As per open_path_mfile, but searching only for local filenames. * This is useful as we may avoid doing a full mfopen and loading * the entire file

* Converts 'in' to a full pathname to store in out. * Out must be at least PATH_MAX bytes long. */

get the length of padding poly As

in principle, this function is only for ChIP-seq target experiment should make target and control inherit from ChIPSeqExperiment, will do

define start and end from gene's transcripts start = min{all starts for transcripts}; end = max{all ends for transcripts};

* Return the cache directory to use, based on the first of these * environment variables to be set to a non-empty value. */

* Count number of successive 0 and 1 bits */

position in the sequence with respect to the aligned part of the read

! @abstract Clear the stream's error indicator */

Called only from hgetc(), when our buffer is empty. */

Called only from hputc(), when our buffer is already full. */

Called only from hputs(), when our buffer is already full. */

Called only from hread(); when called, our buffer is empty and nread bytes have already been placed in the destination buffer. */

* Tokenise options as (key(=value)?,)*(key(=value)?)? * NB: No provision for ',' appearing in the value! * Add backslashing rules? * * This could

hypergeometric distribution

Inflate the block in fp->compressed_block into fp->uncompressed_block

assign threads

Set the initial state