! @abstract Get the color encoding the previous and current base @param b pointer to an alignment @param i The i-th position, 0-based

FIXME: we should also check the LB tag associated with each alignment

! @abstract Merge multiple sorted BAM. @param is_by_qname whether to sort by query name @param out output BAM file name @param m

Notes: - Called from bam_plcmd.c by mpileup. Amongst other things, sets the bcf_callret1_t.qsum frequencies which are carried over via bcf

* 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 the landmarks[] array and the number of elements * in num_landmarks. */

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

*----------------------------------------------------------------------------- * cram_fd */

* Read the next cram record and convert it to a bam_seq_t struct. * * Returns 0 on success * -1 on EOF or failure (check fd->err) */

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

reference_content<T> lacks an implicit conversion to T&, so the following is needed to obtain a proper reference.

Returns the dimension of the sphere. */

em: error model to fit to data m: number of alleles across all samples n: number of bases observed in sample bases[i]: bases observed in pileup [6 bit

* Deallocate an errmod_t object */

* Create errmod_t object with obj.depcorr set to depcorr and initialise */

Filters a header of @RG lines where ID != id_keep TODO: strip @PG's descended from other RGs and their descendants

Given a @RG line return the id