return the sampled position of a given suffix index

--------------------------Whole-Deque Operations-----------------------------| @brief Removes all elements from the priority deque.

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

Compress whatever is at avail_in and next_in and write to the output file. Return -1 if there is an error writing to the output file, otherwise 0.

-- see zlib.h -- */

! @abstract Report the current stream offset @return The offset within the stream, starting from zero. */

Build a set of tables to decode the provided canonical Huffman code. The code lengths are lens[0..codes-1]. The result starts at *table, whose

* Adds a feature code to a read within a slice. For purposes of minimising * memory allocations and fragmentation we have one array of features for a

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

-- see zlib.h -- */

return the local aligner

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

return allocated size

begin iterator

return a syncblocks object

return if the stream is ok

Log gamma function * \log{\Gamma(z)} * AS245, 2nd algorithm, http://lib.stat.cmu.edu/apstat/245 */

get the next batch

convert an ASCII DNA representation to its 2-bit symbol

clear output queues

* Reads a block from a cram file. * Returns cram_block pointer on success. * NULL on failure */

return the end_to_end aligner

=========================================================================== * Fill the window when the lookahead becomes insufficient. * Updates str

========================================================================= * Flush as much pending output as possible. All deflate() output goes * th