If T is of reference type, trying to get a pointer to the held value must result in a compile-time error. Decent compilers should disallow conversions

* cigar_iref2iseq_set() - find the first CMATCH setting the ref and the read index * cigar_iref2iseq_next() - get the next CMATCH base * @cigar:

Confirms the existance of an RG line with a given ID in a bam header

Parse the header, count the number of RG tags and return a list of their names

Offset is known as "size" internally, but it can be confusing.

MAXIMUM storage size needed for the container. */

* Copies the blocks representing the next num_slice slices from a * container from 'in' to 'out'. It is expected that the file pointer * is just af

* Decodes a CRAM (un)mapped slice header block. * Returns slice header ptr on success * NULL on failure */

Opens an existing stream for reading or writing. * * Returns file handle on success; * NULL on failure. */

* Checks whether an external block is used solely by a single data series. * Returns the codec type if so (EXTERNAL, BYTE_ARRAY_LEN, BYTE_ARRAY_STOP)

* Encodes a compression header block into a generic cram_block structure. * * Returns cram_block ptr on success * NULL on failure */

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

* Returns 1 if we hit an EOF while reading. */

* 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 *

* Stores the container structure in dat and returns *size as the * number of bytes written to dat[]. The input size of dat is also * held in *size

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

* Does the work of operator==. This is in a member function * for portability. Some compilers, such as msvc 7.1 and * Sun CC 5.10 can't ac

FIXME: check if the inserted sequence is consistent with the homopolymer run l is the relative gap length and l_run is the length of the homopolymer o

* 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

Expands a output filename format string

* Takes a dirname possibly including % rules and appends the filename * to it. * * Returns expanded pathname or NULL for malloc failure. */

* 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

Returns the appropriate handler, or NULL if the string isn't an URL. */

phase each fragment

n : number of significant digits