* Writes a CRAM block. * Returns 0 on success * -1 on failure */

check whether two alignments are distinct

extract the radices corresponding to a given word of the given suffixes \param n_indices the input number of suffixes \param d_indices

get the next character, or 255 if EOF

incremental version of hypergenometric distribution

convert a range from a [begin,last] representation to a [begin,end) one

merge stats

* Destroys an mFILE structure but does not flush or close it */

return a plain view of a ReadData object

========================================================================= * Put a short in the pending buffer. The 16-bit value is put in MSB order.

read a buffer

alloc enough storage for max_size hits

* Looks for a specific key in a single sam header line. * If prev is non-NULL it also fills this out with the previous tag, to * permit use in key r

Returns the median of three elements. */

* Frees a result 'r' and if free_data is true also frees * the internal r->data result too. */

Returns the median of three elements. */

alloc some slots from a counter using a warp-synchronous reduction

return the average speed

begin iterator

* This processes one or more 64-byte data blocks, but does NOT update * the bit counters. There are no alignment requirements. */

* Seek within a CRAM file. * * Returns 0 on success * -1 on failure */

* * Function: crcInit() * * Description: Populate the partial CRC lookup table. * * Notes: This function must be rerun any time the CRC stan

begin iterator

flush the file

Flushes the write buffer, fp->[buffer,begin), out through the backend returning 0 on success or negative if an error occurred. */

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

Initialize state for writing a gzip file. Mark initialization by setting state->size to non-zero. Return -1 on failure or 0 on success. */

Open a gzip file either by name or file descriptor. */

-- see zlib.h -- */

given a 32-bit word encoding a set of 2-bit symbols, return a submask containing all but the first 'i' entries.