static
rc_t SRAFastqFile_Read(const SRAFastqFile* self, uint64_t pos, void *buffer, size_t size, size_t *num_read)
{
rc_t rc = 0;
if( pos >= self->file_sz ) {
*num_read = 0;
} else if( (rc = KLockAcquire(self->lock)) == 0 ) {
do {
if( pos < self->from || pos >= (self->from + self->size) ) {
int64_t id = 0;
uint64_t id_qty = 0;
DEBUG_MSG(10, ("Caching for pos %lu %lu bytes\n", pos, size - *num_read));
if( (rc = KIndexFindU64(self->kidx, pos, &((SRAFastqFile*)self)->from, &((SRAFastqFile*)self)->size, &id, &id_qty)) == 0 ) {
DEBUG_MSG(10, ("Caching from %lu:%lu, %lu bytes\n", self->from, self->from + self->size - 1, self->size));
DEBUG_MSG(10, ("Caching spot %ld, %lu spots\n", id, id_qty));
if( (rc = FastqReaderSeekSpot(self->reader, id)) == 0 ) {
size_t inbuf = 0, w = 0;
char* b = self->buf;
uint64_t left = self->buffer_sz;
do {
if( (rc = FastqReader_GetCurrentSpotSplitData(self->reader, b, left, &w)) != 0 ) {
break;
}
b += w; left -= w; inbuf += w; --id_qty;
} while( id_qty > 0 && (rc = FastqReaderNextSpot(self->reader)) == 0);
if( GetRCObject(rc) == rcRow && GetRCState(rc) == rcExhausted ) {
DEBUG_MSG(10, ("No more rows\n"));
rc = 0;
}
DEBUG_MSG(8, ("Cached %u bytes\n", inbuf));
if( self->gzipped != NULL ) {
size_t compressed = 0;
if( (rc = ZLib_DeflateBlock(self->buf, inbuf, self->gzipped, self->buffer_sz, &compressed)) == 0 ) {
char* b = self->buf;
((SRAFastqFile*)self)->buf = self->gzipped;
((SRAFastqFile*)self)->gzipped = b;
((SRAFastqFile*)self)->size = compressed;
DEBUG_MSG(10, ("gzipped %lu bytes\n", self->size));
}
}
}
}
}
if( rc == 0 ) {
off_t from = pos - self->from;
size_t q = (self->size - from) > (size - *num_read) ? (size - *num_read) : (self->size - from);
DEBUG_MSG(10, ("Copying from %lu %u bytes\n", from, q));
memcpy(&((char*)buffer)[*num_read], &self->buf[from], q);
*num_read = *num_read + q;
pos += q;
}
} while( rc == 0 && *num_read < size && pos < self->file_sz );
ReleaseComplain(KLockUnlock, self->lock);
}
return rc;
}
static
rc_t FastqGzip_Idx(const SRATable* sratbl, SIndexObj* obj, char* buffer, const size_t buffer_sz)
{
rc_t rc = 0;
const FastqReader* reader = NULL;
uint16_t zlib_ver = ZLIB_VERNUM;
uint8_t colorSpace = false;
char* colorSpaceKey = "\0";
uint8_t origFormat = false;
uint8_t printLabel = true;
uint8_t printReadId = true;
uint8_t clipQuality = true;
uint32_t minReadLen = 0;
uint16_t qualityOffset = 0;
{{
const SRAColumn* c = NULL;
const uint8_t *platform = SRA_PLATFORM_UNDEFINED;
bitsz_t o, z;
if( (rc = SRATableOpenColumnRead(sratbl, &c, "PLATFORM", sra_platform_id_t)) != 0 ) {
return rc;
}
if( (rc = SRAColumnRead(c, 1, (const void **)&platform, &o, &z)) != 0 ) {
return rc;
}
if( *platform == SRA_PLATFORM_ABSOLID ) {
colorSpace = true;
}
SRAColumnRelease(c);
}}
if( (rc = FastqReaderMake(&reader, sratbl, g_accession,
colorSpace, origFormat, false, printLabel, printReadId,
!clipQuality, minReadLen, qualityOffset, colorSpaceKey[0],
obj->minSpotId, obj->maxSpotId)) != 0 ) {
return rc;
} else {
size_t written = 0;
uint32_t blk = 0, spots_per_block = 0, proj_id_qty = 0;
SIndexNode* inode = NULL;
size_t z_blk = 0;
size_t spots_buf_sz = g_file_block_sz * 100;
size_t zbuf_sz = spots_buf_sz + 100;
char* zbuf = malloc(zbuf_sz);
char* spots_buf = malloc(spots_buf_sz);
bool eof = false;
if( zbuf == NULL || spots_buf == NULL ) {
rc = RC(rcExe, rcIndex, rcConstructing, rcMemory, rcExhausted);
}
while( rc == 0 ) {
if( (rc = FastqReader_GetNextSpotSplitData(reader, buffer, buffer_sz, &written)) == 0 ) {
if( inode == NULL ) {
spotid_t spotid = 0;
if( (rc = FastqReaderCurrentSpot(reader, &spotid)) != 0 ) {
break;
}
inode = malloc(sizeof(SIndexNode));
if( inode == NULL ) {
rc = RC(rcExe, rcIndex, rcConstructing, rcMemory, rcExhausted);
break;
}
inode->key = obj->file_size;
inode->key_size = 0;
inode->id = spotid;
inode->id_qty = 0;
DEBUG_MSG(5, ("%s open key: spot %ld, offset %lu\n", obj->index, inode->id, inode->key));
}
if( blk + written > spots_buf_sz ) {
rc = RC(rcExe, rcIndex, rcConstructing, rcMemory, rcInsufficient);
break;
}
inode->id_qty++;
memmove(&spots_buf[blk], buffer, written);
blk += written;
if( g_dump ) {
fwrite(buffer, written, 1, stderr);
}
}
if( (eof = (GetRCObject(rc) == rcRow && GetRCState(rc) == rcExhausted)) ) {
rc = 0;
if( inode == NULL ) {
break;
}
}
if( rc == 0 && (eof ||
(proj_id_qty == 0 && inode->id_qty > (spots_per_block * 0.95)) ||
(proj_id_qty > 0 && inode->id_qty >= proj_id_qty) ) ) {
rc = ZLib_DeflateBlock(spots_buf, blk, zbuf, zbuf_sz, &z_blk);
if( z_blk < g_file_block_sz ) {
/* project needed id_qty */
proj_id_qty = g_file_block_sz * inode->id_qty / z_blk * 1.05;
DEBUG_MSG(5, ("%s: project id qty %u\n", obj->index, proj_id_qty));
} else {
DEBUG_MSG(10, ("%s: no projection %u > %u\n", obj->index, z_blk, g_file_block_sz));
}
}
if( rc == 0 && (eof || z_blk >= g_file_block_sz) ) {
obj->file_size += z_blk;
MD5StateAppend(&obj->md5, zbuf, z_blk);
inode->key_size = z_blk;
SLListPushTail(&obj->li, &inode->n);
DEBUG_MSG(5, ("%s close key: spots %lu, size %lu, ratio %hu%%, raw %u\n",
obj->index, inode->id_qty, inode->key_size, (uint16_t)(((float)(blk - z_blk)/blk)*100), blk ));
spots_per_block = inode->id_qty;
inode = NULL;
if( blk > obj->buffer_sz ) {
obj->buffer_sz = blk;
}
blk = 0;
z_blk = 0;
proj_id_qty = 0;
}
if( eof ) {
break;
}
}
rc = rc ? rc : Quitting();
if( rc != 0 ) {
spotid_t spot = 0;
FastqReaderCurrentSpot(reader, &spot);
PLOGERR(klogErr, (klogErr, rc, "spot $(s)", PLOG_U32(s), spot));
}
free(zbuf);
free(spots_buf);
}
if( rc == 0 ) {
KMDataNode* opt = NULL, *nd = NULL;
if( (rc = KMDataNodeOpenNodeUpdate(obj->meta, &opt, "Format/Options")) != 0 ) {
return rc;
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "ZlibVersion")) == 0 ) {
rc = KMDataNodeWriteB16(nd, &zlib_ver);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "colorSpace")) == 0 ) {
rc = KMDataNodeWriteB8(nd, &colorSpace);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "colorSpaceKey")) == 0 ) {
rc = KMDataNodeWrite(nd, colorSpaceKey, 1);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "origFormat")) == 0 ) {
rc = KMDataNodeWriteB8(nd, &origFormat);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "printLabel")) == 0 ) {
rc = KMDataNodeWriteB8(nd, &printLabel);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "printReadId")) == 0 ) {
rc = KMDataNodeWriteB8(nd, &printReadId);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "clipQuality")) == 0 ) {
rc = KMDataNodeWriteB8(nd, &clipQuality);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "minReadLen")) == 0 ) {
rc = KMDataNodeWriteB32(nd, &minReadLen);
KMDataNodeRelease(nd);
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "qualityOffset")) == 0 ) {
rc = KMDataNodeWriteB16(nd, &qualityOffset);
KMDataNodeRelease(nd);
}
KMDataNodeRelease(opt);
}
FastqReaderWhack(reader);
return rc;
}
static
rc_t SFFGzip_Idx(const SRATable* sratbl, SIndexObj* obj, char* buffer, const size_t buffer_sz)
{
rc_t rc = 0;
uint16_t zlib_ver = ZLIB_VERNUM;
const SFFReader* reader = NULL;
if( (rc = SFFReaderMake(&reader, sratbl, g_accession, obj->minSpotId, obj->maxSpotId)) != 0 ) {
return rc;
} else {
size_t written = 0;
uint32_t blk = 0, spots_per_block = 0, proj_id_qty = 0;
SIndexNode* inode = NULL;
size_t z_blk = 0;
size_t spots_buf_sz = g_file_block_sz * 100;
size_t zbuf_sz = spots_buf_sz + 100;
char* zbuf = malloc(zbuf_sz);
char* spots_buf = malloc(spots_buf_sz);
bool eof = false;
if( zbuf == NULL || spots_buf == NULL ) {
rc = RC(rcExe, rcIndex, rcConstructing, rcMemory, rcExhausted);
}
while( rc == 0 ) {
if( (rc = SFFReader_GetNextSpotData(reader, buffer, buffer_sz, &written)) == 0 ) {
if( inode == NULL ) {
spotid_t spotid = 0;
if( (rc = SFFReaderCurrentSpot(reader, &spotid)) != 0 ) {
break;
}
inode = malloc(sizeof(SIndexNode));
if( inode == NULL ) {
rc = RC(rcExe, rcIndex, rcConstructing, rcMemory, rcExhausted);
break;
}
inode->key = obj->file_size;
inode->key_size = 0;
inode->id = spotid;
inode->id_qty = 0;
DEBUG_MSG(5, ("%s open key: spot %ld, offset %lu\n", obj->index, inode->id, inode->key));
if( spotid == 1 ) {
char hd[10240];
size_t hd_sz = 0;
if( (rc = SFFReaderHeader(reader, 0, hd, sizeof(hd), &hd_sz)) == 0 ) {
if( hd_sz + written > spots_buf_sz ) {
rc = RC(rcExe, rcIndex, rcConstructing, rcMemory, rcInsufficient);
break;
}
memmove(&spots_buf[blk], hd, hd_sz);
blk += hd_sz;
if( g_dump ) {
fwrite(hd, hd_sz, 1, stderr);
}
}
}
}
if( blk + written > spots_buf_sz ) {
rc = RC(rcExe, rcIndex, rcConstructing, rcMemory, rcInsufficient);
break;
}
inode->id_qty++;
memmove(&spots_buf[blk], buffer, written);
blk += written;
if( g_dump ) {
fwrite(buffer, written, 1, stderr);
}
}
if( (eof = (GetRCObject(rc) == rcRow && GetRCState(rc) == rcExhausted)) ) {
rc = 0;
if( inode == NULL ) {
break;
}
}
if( rc == 0 && (eof ||
(proj_id_qty == 0 && inode->id_qty > (spots_per_block * 0.95)) ||
(proj_id_qty > 0 && inode->id_qty >= proj_id_qty) ) ) {
rc = ZLib_DeflateBlock(spots_buf, blk, zbuf, zbuf_sz, &z_blk);
if( z_blk < g_file_block_sz ) {
/* project needed id_qty */
proj_id_qty = g_file_block_sz * inode->id_qty / z_blk * 1.05;
DEBUG_MSG(5, ("%s: project id qty %lu\n", obj->index, proj_id_qty));
} else {
DEBUG_MSG(10, ("%s: no projection %lu > %lu\n", obj->index, z_blk, g_file_block_sz));
}
}
if( rc == 0 && (eof || z_blk >= g_file_block_sz) ) {
obj->file_size += z_blk;
MD5StateAppend(&obj->md5, zbuf, z_blk);
inode->key_size = z_blk;
SLListPushTail(&obj->li, &inode->n);
DEBUG_MSG(5, ("%s close key: spots %lu, size %lu, ratio %hu%%, raw %lu\n",
obj->index, inode->id_qty, inode->key_size, (uint16_t)(((float)(blk - z_blk)/blk)*100), blk));
spots_per_block = inode->id_qty;
inode = NULL;
if( blk > obj->buffer_sz ) {
obj->buffer_sz = blk;
}
blk = 0;
z_blk = 0;
proj_id_qty = 0;
}
if( eof ) {
break;
}
}
rc = rc ? rc : Quitting();
if( rc != 0 ) {
spotid_t spot = 0;
SFFReaderCurrentSpot(reader, &spot);
PLOGERR(klogErr, (klogErr, rc, "spot $(s)", PLOG_U32(s), spot));
}
free(zbuf);
free(spots_buf);
}
if( rc == 0 ) {
KMDataNode* opt = NULL, *nd = NULL;
if( (rc = KMDataNodeOpenNodeUpdate(obj->meta, &opt, "Format/Options")) != 0 ) {
return rc;
}
if( rc == 0 && (rc = KMDataNodeOpenNodeUpdate(opt, &nd, "ZlibVersion")) == 0 ) {
rc = KMDataNodeWriteB16(nd, &zlib_ver);
KMDataNodeRelease(nd);
}
KMDataNodeRelease(opt);
}
SFFReaderWhack(reader);
return rc;
}
