=========================================================================== * Send the block data compressed using the given Huffman trees */

compute the target minimum score for a valid extension of a paired-end alignment

Opens an existing stream for reading or writing. * * Returns file handle on success; * NULL on failure. * * cram_FILE is either htslib's

* Encodes all slices in a container into blocks. * Returns 0 on success * -1 on failure */

* Returns the next 'size' bytes from a block, or NULL if insufficient * data left.This is just a pointer into the block data and not an * allocated

* Flushes a completely or partially full container to disk, writing * container structure, header and blocks. This also calls the encoder * function

common component shared by cram_flush_container{,_mt}

* If fd has been opened for reading, it may be permitted to specify 'fn' * as NULL and let the code auto-detect the reference by parsing the * SAM h

* Loads an entire slice. * FIXME: In 1.0 the native unit of slices within CRAM is broken * as slices contain references to objects in other slices.

* Sets options on the cram_fd. See CRAM_OPT_* definitions in cram_structs.h. * Use this immediately after opening. * * Returns 0 on success *

* Uncompresses a CRAM block, if compressed. */

* Writes a container structure. * * Returns 0 on success * -1 on failure */

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

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

Deflate the block in fp->uncompressed_block into fp->compressed_block. Also adds an extra field that stores the compressed block length.

return the device view of this object

return a view of the queues

implements an inter-CTA synchronization primitive

* Converts a directory and a filename into an expanded path, replacing %s * in directory with the filename and %[0-9]+s with portions of the filename

given a sorted set of n input keys, flags and slots, this function: - updates the set of flags or'ing them with the head flags of the segments of equ

a client method to obtain the given object; once the client has finished using the object, it is responsible to call the release() method to signal co

find the least significant bit set

* Searches for file in the directory 'dirname'. If it finds it, it opens * it. This also searches for compressed versions of the file in dirname * t

find the n-th bit set in a 16-bit mask (n in [1,16])

Return state with length and distance decoding tables and index sizes set to fixed code decoding. Normally this returns fixed tables from inffixed

Frame the opposite mate alignment's direction & orientation \param policy input paired end policy \param anchor 0 iff anchor is mate 1, 1

=========================================================================== * Generate the codes for a given tree and bit counts (which need not be

extract alignment data for the anchor mate

Local optimised copy for inlining */

extract alignment data for a given mate note that the mates can be different for the cigar, since mate 1 is always the anchor mate for cigars

extract alignment data for the opposite mate

get the range of a read in the sequence stream

Load up input buffer and set eof flag if last data loaded -- return -1 on error, 0 otherwise. Note that the eof flag is set when the end of the in

Decompress from input to the provided next_out and avail_out in the state. On return, state->x.have and state->x.next point to the just decompresse

Look for gzip header, set up for inflate or copy. state->x.have must be 0. If this is the first time in, allocate required memory. state->how wil

Reset gzip file state */

-- see zlib.h -- */

-- see zlib.h -- */

given a 64-bit word encoding a set of 2-bit symbols, return a submask containing all but the first 'i' entries.

return the number of allocated hits

! @abstract Write a character to the stream @return The character written, or EOF if an error occurred. */

Called only from hwrite() and hputs2(); when called, our buffer is full and ncopied bytes from the source have already been copied to our buffer.

return the offset this iterator refers to

Decode literal, length, and distance codes and write out the resulting literal and match bytes until either not enough input or output is availa

initializes a SAM file will consume the SAM header and prepare for fetching reads from the file returns false on failure

=========================================================================== * Initialize a new block. */

initialize extraction of a slice of words

* Decodes a 32-bit little endian value from fd and stores in val. * * Returns the number of bytes read on success * -1 on failure */

Returns whether the block contains any control characters, i.e., characters less than SPACE other than whitespace etc (ASCII BEL..CR).