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/*
* Copyright (c) 2005, 2007-2010 Genome Research Ltd.
* Author(s): James Bonfield
*
* 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.
*/
/*
* Portions of this code have been derived from 454 Life Sciences Corporation's
* getsff.c code (specifically the WriteSFFFile function.
* It bears the following copyright notice:
*
* ------------------------------------------------------------
* Copyright (c)[2001-2005] 454 Life Sciences Corporation. All Rights Reserved.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
*
* IN NO EVENT SHALL LICENSOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE.
*
* Permission to use, copy, modify and distribute this software and its
* documentation for any purpose is hereby granted without fee, provided
* that this copyright and notice appears in all copies.
* ------------------------------------------------------------
*
* The remainder is Copyright Genome Research Limited (GRL) and is covered
* by a BSD style license as described elsewhere in this source tree.
*/
#ifdef HAVE_CONFIG_H
#include "io_lib_config.h"
#endif
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "io_lib/Read.h"
#include "io_lib/xalloc.h"
#include "io_lib/sff.h"
#include "io_lib/misc.h"
/* -------------------------------------------------------------------------*/
/* General purpose decoding and mFILE reading functions */
/*
* Unpacks the 31-byte fixed size part of the SFF common header.
* It allocates memory for this and for the flow order and key, but does
* not read the flow & key information (as this may not be in buf).
* It also checks that the MAGIC and VERSION match as expected.
*
* Returns sff_common_header* on success
* NULL on failure
*/
sff_common_header *decode_sff_common_header(unsigned char *buf) {
sff_common_header *h;
if (NULL == (h = (sff_common_header *)xcalloc(1, sizeof(*h))))
return NULL;
h->magic = be_int4(*(uint32_t *)(buf+0));
memcpy(h->version, buf+4, 4);
h->index_offset = be_int8(*(uint64_t *)(buf+8));
h->index_len = be_int4(*(uint32_t *)(buf+16));
h->nreads = be_int4(*(uint32_t *)(buf+20));
h->header_len = be_int2(*(uint16_t *)(buf+24));
h->key_len = be_int2(*(uint16_t *)(buf+26));
h->flow_len = be_int2(*(uint16_t *)(buf+28));
h->flowgram_format = be_int1(*(uint8_t *)(buf+30));
if (h->magic != SFF_MAGIC || memcmp(h->version, SFF_VERSION, 4)) {
xfree(h);
return NULL;
}
if (NULL == (h->flow = (char *)xmalloc(h->flow_len)))
return free_sff_common_header(h), NULL;
if (NULL == (h->key = (char *)xmalloc(h->key_len)))
return free_sff_common_header(h), NULL;
return h;
}
/*
* Encodes the data in 'h' to the file SFF representation. Buf should be
* allocated to be 31 + h->flow_len + h->key_len + 8.
*
* Returns: the written length of buf
*/
int encode_sff_common_header(sff_common_header *h, unsigned char *buf) {
int end;
*(uint32_t *)(buf+0) = be_int4(h->magic);
memcpy(buf+4, h->version, 4);
*(uint64_t *)(buf+8) = be_int8(h->index_offset);
*(uint32_t *)(buf+16) = be_int4(h->index_len);
*(uint32_t *)(buf+20) = be_int4(h->nreads);
*(uint16_t *)(buf+24) = be_int2(h->header_len);
*(uint16_t *)(buf+26) = be_int2(h->key_len);
*(uint16_t *)(buf+28) = be_int2(h->flow_len);
*(uint8_t *)(buf+30) = be_int1(h->flowgram_format);
memcpy(buf+31, h->flow, h->flow_len);
memcpy(buf+31+h->flow_len, h->key, h->key_len);
end = 31+h->flow_len+h->key_len;
memcpy(buf+end, "\0\0\0\0\0\0\0\0", ((end+7)&~7)-end);
return (end+7)&~7;
}
/*
* Reads a common header (including variable length components) from an mFILE.
*
* Returns the a pointer to the header on success
* NULL on failure
*/
sff_common_header *read_sff_common_header(mFILE *mf) {
sff_common_header *h;
unsigned char chdr[31];
if (31 != mfread(chdr, 1, 31, mf))
return NULL;
h = decode_sff_common_header(chdr);
if (h->flow_len != mfread(h->flow, 1, h->flow_len, mf))
return free_sff_common_header(h), NULL;
if (h->key_len != mfread(h->key , 1, h->key_len, mf))
return free_sff_common_header(h), NULL;
/* Pad to 8 chars */
mfseek(mf, (mftell(mf) + 7)& ~7, SEEK_SET);
return h;
}
/*
* Deallocates memory used by an SFF common header.
*/
void free_sff_common_header(sff_common_header *h) {
if (!h)
return;
if (h->flow)
xfree(h->flow);
if (h->key)
xfree(h->key);
xfree(h);
}
/*
* Unpacks the 16-byte fixed size part of the SFF read header.
* It allocates memory for this and for the base calls, but does not
* unpack these.
*
* Returns sff_read_header* on success
* NULL on failure
*/
sff_read_header *decode_sff_read_header(unsigned char *buf) {
sff_read_header *h;
if (NULL == (h = (sff_read_header *)xcalloc(1, sizeof(*h))))
return NULL;
h->header_len = be_int2(*(uint16_t *)(buf+0));
h->name_len = be_int2(*(uint16_t *)(buf+2));
h->nbases = be_int4(*(uint32_t *)(buf+4));
h->clip_qual_left = be_int2(*(uint16_t *)(buf+8));
h->clip_qual_right = be_int2(*(uint16_t *)(buf+10));
h->clip_adapter_left = be_int2(*(uint16_t *)(buf+12));
h->clip_adapter_right = be_int2(*(uint16_t *)(buf+14));
if (NULL == (h->name = (char *)xmalloc(h->name_len)))
return free_sff_read_header(h), NULL;
return h;
}
/*
* Encodes the data in 'h' to the file SFF representation. Buf should be
* allocated to be 16 + h->name_len + 8.
*
* Returns: the written length of buf
*/
int encode_sff_read_header(sff_read_header *h, unsigned char *buf) {
int end;
*(uint16_t *)(buf+0) = be_int2(h->header_len);
*(uint16_t *)(buf+2) = be_int2(h->name_len);
*(uint32_t *)(buf+4) = be_int4(h->nbases);
*(uint16_t *)(buf+8) = be_int2(h->clip_qual_left);
*(uint16_t *)(buf+10) = be_int2(h->clip_qual_right);
*(uint16_t *)(buf+12) = be_int2(h->clip_adapter_left);
*(uint16_t *)(buf+14) = be_int2(h->clip_adapter_right);
memcpy(buf+16, h->name, h->name_len);
end = 16+h->name_len;
memcpy(buf+end, "\0\0\0\0\0\0\0\0", ((end+7)&~7)-end);
return (end+7)&~7;
}
/*
* Reads a read header (including variable length components) from an mFILE.
*
* Returns the a pointer to the header on success
* NULL on failure
*/
sff_read_header *read_sff_read_header(mFILE *mf) {
sff_read_header *h;
unsigned char rhdr[16];
if (16 != mfread(rhdr, 1, 16, mf))
return NULL;
h = decode_sff_read_header(rhdr);
if (h->name_len != mfread(h->name, 1, h->name_len, mf))
return free_sff_read_header(h), NULL;
/* Pad to 8 chars */
mfseek(mf, (mftell(mf) + 7)& ~7, SEEK_SET);
return h;
}
/*
* Deallocates memory used by an SFF read header
*/
void free_sff_read_header(sff_read_header *h) {
if (!h)
return;
if (h->name)
xfree(h->name);
free(h);
}
/*
* Reads a read data block from an mFILE given a count of the number of
* flows and basecalls (from the common header and read headers).
*
* Returns the a pointer to sff_read_data on success
* NULL on failure
*/
sff_read_data *read_sff_read_data(mFILE *mf, int nflows, int nbases) {
sff_read_data *d;
int i;
if (NULL == (d = (sff_read_data *)xcalloc(1, sizeof(*d))))
return NULL;
if (NULL == (d->flowgram = (uint16_t *)xcalloc(nflows, 2)))
return free_sff_read_data(d), NULL;
if (nflows != mfread(d->flowgram, 2, nflows, mf))
return free_sff_read_data(d), NULL;
for (i = 0; i < nflows; i++)
d->flowgram[i] = be_int2(d->flowgram[i]);
if (NULL == (d->flow_index = (uint8_t *)xmalloc(nbases)))
return free_sff_read_data(d), NULL;
if (nbases != mfread(d->flow_index, 1, nbases, mf))
return free_sff_read_data(d), NULL;
if (NULL == (d->bases = (char *)xmalloc(nbases)))
return free_sff_read_data(d), NULL;
if (nbases != mfread(d->bases, 1, nbases, mf))
return free_sff_read_data(d), NULL;
if (NULL == (d->quality = (uint8_t *)xmalloc(nbases)))
return free_sff_read_data(d), NULL;
if (nbases != mfread(d->quality, 1, nbases, mf))
return free_sff_read_data(d), NULL;
/* Pad to 8 chars */
mfseek(mf, (mftell(mf) + 7)& ~7, SEEK_SET);
return d;
}
/*
* Deallocates memory used by an SFF read data block
*/
void free_sff_read_data(sff_read_data *d) {
if (!d)
return;
if (d->flowgram)
xfree(d->flowgram);
if (d->flow_index)
xfree(d->flow_index);
if (d->bases)
xfree(d->bases);
if (d->quality)
xfree(d->quality);
xfree(d);
}
/* -------------------------------------------------------------------------*/
/*
* Reads an SFF file from an mFILE and decodes it to a Read struct.
*
* Returns Read* on success
* NULL on failure
*/
Read *mfread_sff(mFILE *mf) {
int i, bpos;
Read *r;
sff_common_header *ch;
sff_read_header *rh;
sff_read_data *rd;
/* Load the SFF contents */
if (NULL == (ch = read_sff_common_header(mf)))
return NULL;
if (NULL == (rh = read_sff_read_header(mf))) {
free_sff_common_header(ch);
return NULL;
}
if (NULL == (rd = read_sff_read_data(mf, ch->flow_len, rh->nbases))) {
free_sff_common_header(ch);
free_sff_read_header(rh);
return NULL;
}
/* Convert to Read struct */
r = read_allocate(0,0);
if (r->basePos) free(r->basePos);
if (r->base) free(r->base);
if (r->prob_A) free(r->prob_A);
if (r->prob_C) free(r->prob_C);
if (r->prob_G) free(r->prob_G);
if (r->prob_T) free(r->prob_T);
r->nflows = ch->flow_len;
r->flow_order = ch->flow; ch->flow = NULL;
r->flow_raw = NULL;
r->flow = (float *)malloc(r->nflows * sizeof(float));
for (i = 0; i < r->nflows; i++) {
r->flow[i] = rd->flowgram[i] / 100.0;
}
r->NBases = rh->nbases;
r->basePos = (uint_2 *)calloc(r->NBases, 2);
r->base = rd->bases; rd->bases = NULL;
r->prob_A = (char *)calloc(r->NBases, 1);
r->prob_C = (char *)calloc(r->NBases, 1);
r->prob_G = (char *)calloc(r->NBases, 1);
r->prob_T = (char *)calloc(r->NBases, 1);
bpos = 0;
for (i=0; i < r->NBases; i++) {
r->prob_A[i] = 0;
r->prob_C[i] = 0;
r->prob_G[i] = 0;
r->prob_T[i] = 0;
switch (r->base[i]) {
case 'A':
case 'a':
r->prob_A[i] = rd->quality[i];
break;
case 'C':
case 'c':
r->prob_C[i] = rd->quality[i];
break;
case 'G':
case 'g':
r->prob_G[i] = rd->quality[i];
break;
case 'T':
case 't':
r->prob_T[i] = rd->quality[i];
break;
}
bpos += rd->flow_index[i];
r->basePos[i] = bpos;
}
r->leftCutoff = MAX(rh->clip_qual_left, rh->clip_adapter_left);
r->rightCutoff = MIN(rh->clip_qual_right
? rh->clip_qual_right
: r->NBases+1,
rh->clip_adapter_right
? rh->clip_adapter_right
: r->NBases+1);
free_sff_common_header(ch);
free_sff_read_header(rh);
free_sff_read_data(rd);
return r;
}
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