Local optimised copy for inlining */

These are to be replaced by samtools header parser Extracts the first @RG line from a string.

Returns a copy of the value if this is initialized, 'v' otherwise

! @abstract Return the stream's error indicator @return Non-zero (in fact, an errno value) if an error has occurred. @notes This would b

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

For VCF/BCF backward sweeper. Not exposing these functions because their future is uncertain. Things will probably have to change with hFILE...

* Tokenise options as (key(=value)?,)*(key(=value)?)? * NB: No provision for ',' appearing in the value! * Add backslashing rules? * * This could

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.

* Encodes a 32-bit little endian value 'val' and writes to fd. * * Returns the number of bytes written on success * -1 on failure */

These helper functions are used only when numeric_limits<> members are not compile time constants:

Returns the @c k parameter of the distribution. */

Destroy a bit set.

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

Insert an element into the bit set.

Regularized incomplete beta function. The method is taken from * Numerical Recipe in C, 2nd edition, section 6.4. The following web * page calculate

place ->fd at offset off

* Destroys both the hash structure and the keys */

* Set a new key,value pair. On success returns the bin index, on * error -1 is returned. Note that the key must contnue to exist * throughout the

In windows, the first thing is to establish the TCP connection. */

Append a kstring to a kstring

Returns the lambda parameter of the distribution. */

* Used by cram_ref_load and cram_ref_get. The file handle will have * already been opened, so we can catch it. The ref_entry *e informs us * of whet

Returns the m parameter of the distribution. */

Returns the "m" parameter of the distribution. */

* Quick and simple hash lookup for cram_map arrays */