143 lines
4.5 KiB
C
143 lines
4.5 KiB
C
/*
|
|
Copyright (c) 2012-2013, 2018, 2024 Genome Research Ltd.
|
|
Author: James Bonfield <jkb@sanger.ac.uk>
|
|
|
|
Redistribution and use in source and binary forms, with or without
|
|
modification, are permitted provided that the following conditions are met:
|
|
|
|
1. Redistributions of source code must retain the above copyright notice,
|
|
this list of conditions and the following disclaimer.
|
|
|
|
2. Redistributions in binary form must reproduce the above copyright notice,
|
|
this list of conditions and the following disclaimer in the documentation
|
|
and/or other materials provided with the distribution.
|
|
|
|
3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
|
|
Institute nor the names of its contributors may be used to endorse or promote
|
|
products derived from this software without specific prior written permission.
|
|
|
|
THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
|
|
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
|
|
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
|
|
DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
|
|
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
|
|
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
|
|
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
|
|
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
|
|
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
|
|
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
|
*/
|
|
|
|
/*! \file
|
|
* Include cram.h instead.
|
|
*
|
|
* This is an internal part of the CRAM system and is automatically included
|
|
* when you #include cram.h.
|
|
*
|
|
* Implements the decoding portion of CRAM I/O. Also see
|
|
* cram_codecs.[ch] for the actual encoding functions themselves.
|
|
*/
|
|
|
|
#ifndef CRAM_DECODE_H
|
|
#define CRAM_DECODE_H
|
|
|
|
#ifdef __cplusplus
|
|
extern "C" {
|
|
#endif
|
|
|
|
/* ----------------------------------------------------------------------
|
|
* CRAM sequence iterators.
|
|
*/
|
|
|
|
/*! Read the next cram record and return it as a cram_record.
|
|
*
|
|
* Note that to decode cram_record the caller will need to look up some data
|
|
* in the current slice, pointed to by fd->ctr->slice. This is valid until
|
|
* the next call to cram_get_seq (which may invalidate it).
|
|
*
|
|
* @return
|
|
* Returns record pointer on success (do not free);
|
|
* NULL on failure
|
|
*/
|
|
cram_record *cram_get_seq(cram_fd *fd);
|
|
|
|
/*! Read the next cram record and convert it to a bam_seq_t struct.
|
|
*
|
|
* @return
|
|
* Returns 0 on success;
|
|
* -1 on EOF or failure (check fd->err)
|
|
*/
|
|
int cram_get_bam_seq(cram_fd *fd, bam_seq_t **bam);
|
|
|
|
|
|
/* ----------------------------------------------------------------------
|
|
* Internal functions
|
|
*/
|
|
|
|
/*! INTERNAL:
|
|
* Decodes a CRAM block compression header.
|
|
*
|
|
* @return
|
|
* Returns header ptr on success;
|
|
* NULL on failure
|
|
*/
|
|
cram_block_compression_hdr *cram_decode_compression_header(cram_fd *fd,
|
|
cram_block *b);
|
|
|
|
/*! INTERNAL:
|
|
* Decodes a CRAM (un)mapped slice header block.
|
|
*
|
|
* @return
|
|
* Returns slice header ptr on success;
|
|
* NULL on failure
|
|
*/
|
|
cram_block_slice_hdr *cram_decode_slice_header(cram_fd *fd, cram_block *b);
|
|
|
|
|
|
/*! INTERNAL:
|
|
* Loads and decodes the next slice worth of data.
|
|
*
|
|
* @return
|
|
* Returns cram slice pointer on success;
|
|
* NULL on failure
|
|
*/
|
|
cram_slice *cram_next_slice(cram_fd *fd, cram_container **cp);
|
|
|
|
/*! INTERNAL:
|
|
* Decode an entire slice from container blocks. Fills out s->crecs[] array.
|
|
*
|
|
* @return
|
|
* Returns 0 on success;
|
|
* -1 on failure
|
|
*/
|
|
int cram_decode_slice(cram_fd *fd, cram_container *c, cram_slice *s,
|
|
sam_hdr_t *hdr);
|
|
|
|
|
|
/*! INTERNAL:
|
|
* 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 allocated size. These can initially be pointers to NULL and zero.
|
|
*
|
|
* This function will reallocate the bam buffer as required and update
|
|
* (*bam)->alloc accordingly, allowing it to be used within a loop
|
|
* efficiently without needing to allocate new bam objects over and
|
|
* over again.
|
|
*
|
|
* Returns the used size of the bam record on success
|
|
* -1 on failure.
|
|
*/
|
|
int cram_to_bam(sam_hdr_t *sh, cram_fd *fd, cram_slice *s,
|
|
cram_record *cr, int rec, bam_seq_t **bam);
|
|
|
|
/*
|
|
* Drains and frees the decode read-queue for a multi-threaded reader.
|
|
*/
|
|
void cram_drain_rqueue(cram_fd *fd);
|
|
|
|
#ifdef __cplusplus
|
|
}
|
|
#endif
|
|
|
|
#endif
|