writes the supplied data into the BGZF buffer

writes the supplied data into the BGZF buffer

* Returns index of val into key. * Basically strchr(key, val)-key; */

Give ownership of the underlying buffer away to something else (making that something else responsible for freeing it), leaving the kstring_t empty an

* Processes a standard "global" samtools long option. * * The 'c' value is the return value from a getopt_long() call. It is checked * against the

* Report the usage for global options. * * This accepts a string with one character per SAM_OPT_GLOBAL_OPTIONS option * to determine which options

copy buffer to string :

* Compresses a block using one of two different zlib strategies. If we only * want one choice set strat2 to be -1. * * The logic here is that somet

Encodes a given symbol. This is faster than straight RansEnc since we can do multiplications instead of a divide. See RansEncSymbolInit for a descrip

at() with range check

s MUST BE returned by bam_aux_get()

! @abstract Report the current stream offset @return The offset within the stream, starting from zero. */

* Reads a block from a cram file. * Returns cram_block pointer on success. * NULL on failure */

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

makes no sense for noise gene

Test whether the bit set contains the element.

interval : [,) random number should be in [0, arr[len - 1]) If by chance arr[len - 1] == 0.0, one possibility is to sample uniformly from 0 ... len -

front() and back()

Eid: external sid

reads BGZF data into a byte buffer

reads BGZF data into a byte buffer

* Adds a feature code to a read within a slice. For purposes of minimising * memory allocations and fragmentation we have one array of features for a