* Opens a reference fasta file as a BGZF stream, allowing for * compressed files. It automatically builds a .fai file if * required and if compress

Returns: 0 on success (BGZF header); -1 on non-BGZF GZIP header; -2 on error

* Decode an entire slice from container blocks. Fills out s->crecs[] array. * Returns 0 on success * -1 on failure */

* Read the next cram record and convert it to a bam_seq_t struct. * * Returns >= 0 success (number of bytes written to *bam) * -1 on EOF or

* Creates a new container, specifying the maximum number of slices * and records permitted. * * Returns cram_container ptr on success * NU

* During cram_next_container or before the final flush at end of * file, we update the current slice headers and increment the slice * number to the

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

Local optimised copy for inlining */

Clear the stream's error indicator

Write a string to the stream @return 0 if successful, or `EOF` if an error occurred. */

* Wakes up a single thread stuck in dispatch and make it return with * errno EAGAIN. */

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

Store a uint16_t value in little-endian byte order @param val The value to store * @param buf Where to store it (may be unaligned) */

change it back just before output;

* Encodes and writes a single integer in ITF-8 format. * Returns 0 on success * -1 on failure */

Initialise an empty bit set capable of holding ni integers, 0 <= i < ni.

Insert an element into the bit set.

* Destroys both the hash structure and the keys */

* Add a new string to the dictionary, auto-incrementing the value. * On success returns the newly inserted integer id, on error -1 * is returned.

log\binom{n}{k}

log\binom{n}{k}

Get a double value from an unsigned byte array @param buf Pointer to source byte array, may be unaligned * @return A 64 bit floating point value *

Get an int8_t value from an unsigned byte array @param buf Pointer to source byte array, may be unaligned * @return A 8 bit signed integer * The i

----------------------------------------------------------------------------- * Simple interface to the order-0 vs order-1 encoders and decoders. */

* Frees/unmaps a reference sequence and associated file handles. */

* Indexes references by the order they appear in a BAM file. This may not * necessarily be the same order they appear in the fasta reference file. *

* Looks up a read-group by name and returns a pointer to the start of the * associated tag list. * * Returns NULL on failure */

* Tokenises a SAM header into a hash table. * Also extracts a few bits on specific data types, such as @RG lines. * * Returns a SAM_hdr struct on s