* A specialised form of cram_index_build (below) that deals with slices * having multiple references in this (ref_id -2). In this scenario we * deco

* Loads a CRAM .crai index into memory. * * Returns 0 for success * -1 for failure */

* Searches the index for the first slice overlapping a reference ID * and position, or one immediately preceding it if none is found in * the index

* Initialises the lookup tables. These could be global statics, but they're * clumsy to setup in a multi-threaded environment unless we generate * v

* Creates a new blank container compression header * * Returns header ptr on success * NULL on failure */

* Creates a new empty slice in memory, for subsequent writing to * disk. * * Returns cram_slice ptr on success * NULL on failure */

* Handles creation of a new container or new slice, flushing any * existing containers when appropriate. * * Really this is next slice, which may

* Here be dragons! The multi-threading code in this is crufty beyond belief. */

* Queries the M5 string from the header and attempts to populate the * reference from this using the REF_PATH environment. * * Returns 0 on sucess

* Write iterator: put BAM format sequences into a CRAM file. * We buffer up a containers worth of data at a time. * * Returns 0 on success *

* Reads the SAM header from the first CRAM data block. * Also performs minimal parsing to extract read-group * and sample information. * Returns S

* Reads a CRAM file definition structure. * Returns file_def ptr on success * NULL on failure */

* Load the entire reference 'id'. * This also increments the reference count by 1. * * Returns ref_entry on success; * NULL on failure */

* Reads a file and outputs a new CRAM file to stdout with 'h' * replaced as the header. No checks are made to the validity. * * FIXME: error check

* Reads a version 2 CRAM file and replaces the header in-place, * provided the header is small enough to fit without growing the * entire file. *

* Reads a version 3 CRAM file and replaces the header in-place, * provided the header is small enough to fit without growing the * entire file. *

* Skips to a container overlapping the start coordinate listed in * cram_range. * * In theory we call cram_index_query multiple times, once per sli

* Attaches a header to a cram_fd. * * This should be used when creating a new cram_fd for writing where * we have an SAM_hdr already constructed (e

*----------------------------------------------------------------------------- * cram_slice */

* Converts a cram in-memory record into a bam in-memory record. We * pass a pointer to a bam_seq_t pointer along with the a pointer to * the allocat

* Renumbers RG numbers in a cram compression header. * * CRAM stores RG as the Nth number in the header, rather than a * string holding the ID: tag

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

* Writes a cram_file_def structure to cram_fd. * Returns 0 on success * -1 on failure */

Decompress up to ten or so bytes by peeking at the file, which must be positioned at the start of a GZIP block.

define TSS and TES

Begin by defining the smallest value for which it is safe to use the asymptotic expansion for digamma:

phasing

gseq : genomic sequence