static rc_t Run(const CmdLine* args)
{
rc_t rc = 0;
Db db;
SpotIterator it;
assert(args);
if (!SpotIteratorFileExists(args->file)) {
rc = RC(rcExe, rcFile, rcOpening, rcFile, rcNotFound);
PLOGERR(klogErr,
(klogErr, rc, "Cannot find '$(path)'", "path=%s", args->file));
}
else if (!SpotIteratorFileExists(args->table)) {
rc = RC(rcExe, rcTable, rcOpening, rcTable, rcNotFound);
PLOGERR(klogErr,
(klogErr, rc, "Cannot find '$(path)'", "path=%s", args->table));
}
{
rc_t rc2 = DbInit(rc, args, &db);
if (rc == 0)
{ rc = rc2; }
}
if (rc == 0) {
rc = SpotIteratorInit(args->file, &db, &it);
}
if (rc == 0) {
rc = Work(&db, &it);
}
if (rc == 0) {
PLOGMSG(klogInfo, (klogInfo,
"Success: redacted $(redacted) spots out of $(all)",
"redacted=%d,all=%d", db.redactedSpots, db.nSpots));
}
{
rc_t rc2 = SpotIteratorDestroy(&it);
if (rc == 0)
{ rc = rc2; }
}
{
rc_t rc2 = DbDestroy(&db);
if (rc == 0)
{ rc = rc2; }
}
return rc;
}
static rc_t SDataUpdate(struct SData* self,
const char* newColName, const char* redactFileName,
spotid_t* redactedSpots, spotid_t* all)
{
struct SBlob blob;
uint8_t filter[32];
rc_t rc = 0, rc2 = 0;
uint32_t colIdx = 0;
spotid_t spot = 0, last = 0;
bool toRedact = false;
struct SpotIterator it;
assert(self && redactedSpots && all);
memset(filter, SRA_READ_FILTER_REDACTED, sizeof filter);
if ((rc = SpotIteratorInit(&it, self->_rdTbl, redactFileName))
== 0)
{
rc = SRATableOpenColumnWrite
(self->_wrTbl, &colIdx, NULL, newColName, sra_read_filter_t);
if (rc != 0) {
plogerr(klogErr, rc,
"cannot open Column $(path) for Write", "path=%s", newColName);
return rc;
}
}
else {
return rc;
}
rc = SBlobInit(&blob, self, &it);
if (rc != 0) {
return rc;
}
while (rc == 0 && SpotIteratorNext(&it, &rc, &spot, &toRedact)) {
bitsz_t offset = 0, size = 0;
const void *base = NULL;
uint8_t nReads = 0;
if (rc != 0) {
break;
}
plogmsg(klogDebug2, "Spot $(spot): $(action)",
PLOG_U32(spot) ",action=%s",
spot, toRedact ? "redact" : "original");
/* GET NEXT BLOB RANGE */
if (spot == 1 || spot > last) {
rc = SBlobGetRange(&blob, spot, &last);
if (rc != 0) {
break;
}
}
assert(spot <= last);
/* GET NREADS */
if ((rc = SRAColumnRead
(self->_NReadsCol, spot, &base, &offset, &size)) != 0)
{
logerr(klogErr, rc, "cannot SRAColumnRead");
break;
}
else if (offset != 0 || size != sizeof nReads * 8) {
rc = RC(rcExe, rcColumn, rcReading, rcData, rcInvalid);
plogerr(klogErr, rc,
"Bad SRAColumnRead(\"NREADS\", $(spot)) result",
PLOG_U32(spot), spot);
}
else {
nReads = *((uint8_t*) base);
if (spot == 1) {
if (nReads == 1) {
plogmsg(klogInfo, "The first spot has $(nreads) read",
"nreads=%d", nReads);
}
else {
plogmsg(klogInfo, "The first spot has $(nreads) reads",
"nreads=%d", nReads);
}
}
}
/* GET READ_FILTER */
if (toRedact) {
base = filter;
++(*redactedSpots);
}
else {
if ((rc = SRAColumnRead(self->_origFilterCol,
spot, &base, &offset, &size)) != 0)
{
plogerr(klogErr, rc,
"while calling SRAColumnRead($(name))", "name=%s",
"READ_FILTER");
break;
}
else if (offset != 0
|| size != sizeof (uint8_t) * 8 * nReads)
{
rc = RC(rcExe, rcColumn, rcReading, rcData, rcInvalid);
plogerr(klogErr, rc, "Bad SRAColumnRead($(spot)) result",
PLOG_U32(spot), spot);
}
}
if ((rc = SRATableOpenSpot(self->_wrTbl, spot)) != 0) {
plogerr(klogErr, rc, "cannot open Spot $(id)", PLOG_U32(id), spot);
break;
}
if ((rc = SRATableWriteIdxColumn(self->_wrTbl,
colIdx, base, 0, sizeof (uint8_t) * 8 * nReads)) != 0)
{
logerr(klogErr, rc, "cannot SRATableWriteIdxColumn");
break;
}
if ((rc = SRATableCloseSpot(self->_wrTbl)) != 0) {
logerr(klogErr, rc, "cannot SRATableCloseSpot");
break;
}
/* CUT THE BLOB */
if (spot == last) {
rc = SRATableCloseCursor(self->_wrTbl);
if (rc != 0) {
plogerr(klogErr, rc, "cannot SRATableCloseCursor $(id)",
PLOG_U32(id), spot);
break;
}
}
}
rc2 = SpotIteratorDestroy(&it);
if (rc == 0)
{ rc = rc2; }
*all = spot;
return rc;
}
