errorCode decodeDecimalValue(EXIStream* strm, Decimal* dec_val)
{
errorCode tmp_err_code = EXIP_UNEXPECTED_ERROR;
boolean sign;
UnsignedInteger integr_part = 0;
UnsignedInteger fract_part = 0;
UnsignedInteger fract_part_rev = 0;
unsigned int e;
DEBUG_MSG(INFO, DEBUG_STREAM_IO, (">> (decimal)"));
// TODO: implement checks on type overflow
TRY(decodeBoolean(strm, &sign));
TRY(decodeUnsignedInteger(strm, &integr_part));
TRY(decodeUnsignedInteger(strm, &fract_part));
dec_val->exponent = 0;
fract_part_rev = 0;
while(fract_part > 0)
{
fract_part_rev = fract_part_rev*10 + fract_part%10;
fract_part = fract_part/10;
dec_val->exponent -= 1;
}
if(sign == TRUE) // negative number
dec_val->mantissa = -1;
else
dec_val->mantissa = 1;
dec_val->mantissa *= integr_part;
e = dec_val->exponent;
if(e != 0)
{
while(e)
{
dec_val->mantissa *= 10;
e++;
}
dec_val->mantissa += fract_part_rev;
}
return EXIP_OK;
}
errorCode decodeIntegerValue(EXIStream* strm, Integer* sint_val)
{
// TODO: If there is associated schema datatype handle differently!
// TODO: check if the result fit into int type
errorCode tmp_err_code = EXIP_UNEXPECTED_ERROR;
boolean bool_val = 0;
UnsignedInteger val;
DEBUG_MSG(INFO, DEBUG_STREAM_IO, (">> (int)"));
TRY(decodeBoolean(strm, &bool_val));
TRY(decodeUnsignedInteger(strm, &val));
if(bool_val == 0) // A sign value of zero (0) is used to represent positive integers
*sint_val = (Integer) val;
else if(bool_val == 1) // A sign value of one (1) is used to represent negative integers
{
val += 1;
*sint_val = -((Integer) val);
}
else
return EXIP_UNEXPECTED_ERROR;
return EXIP_OK;
}
void
gkLibrary::gkLibrary_setFeature(char *fea, char *val) {
// Unitigger options
if (strcasecmp(fea, "forceBOGunitigger") == 0)
forceBOGunitigger = decodeBoolean("forceBOGunitigger", val);
else if (strcasecmp(fea, "isNotRandom") == 0)
isNotRandom = decodeBoolean("isNotRandom", val);
// Alignment options
else if (strcasecmp(fea, "doNotTrustHomopolymerRuns") == 0)
doNotTrustHomopolymerRuns = decodeBoolean("doNotTrustHomopolymerRuns", val);
// OBT options
else if (strcasecmp(fea, "doTrim_initialNone") == 0)
doTrim_initialNone = decodeBoolean("doTrim_initialNone", val);
else if (strcasecmp(fea, "doTrim_initialMerBased") == 0)
doTrim_initialMerBased = decodeBoolean("doTrim_initialMerBased", val);
else if (strcasecmp(fea, "doTrim_initialFlowBased") == 0)
doTrim_initialFlowBased = decodeBoolean("doTrim_initialFlowBased", val);
else if (strcasecmp(fea, "doTrim_initialQualityBased") == 0)
doTrim_initialQualityBased = decodeBoolean("doTrim_initialQualityBased", val);
else if (strcasecmp(fea, "doRemoveDuplicateReads") == 0)
doRemoveDuplicateReads = decodeBoolean("doRemoveDuplicateReads", val);
else if (strcasecmp(fea, "doTrim_finalLargestCovered") == 0)
doTrim_finalLargestCovered = decodeBoolean("doTrim_finalLargestCovered", val);
else if (strcasecmp(fea, "doTrim_finalEvidenceBased") == 0)
doTrim_finalEvidenceBased = decodeBoolean("doTrim_finalEvidenceBased", val);
else if (strcasecmp(fea, "doTrim_finalBestEdge") == 0)
doTrim_finalBestEdge = decodeBoolean("doTrim_finalBestEdge", val);
else if (strcasecmp(fea, "doRemoveSpurReads") == 0)
doRemoveSpurReads = decodeBoolean("doRemoveSpurReads", val);
else if (strcasecmp(fea, "doRemoveChimericReads") == 0)
doRemoveChimericReads = decodeBoolean("doRemoveChimericReads", val);
else if (strcasecmp(fea, "doCheckForSubReads") == 0)
doCheckForSubReads = decodeBoolean("doCheckForSubReads", val);
// COMPATIBILITY OPTIONS
else if (strcasecmp(fea, "doMerBasedTrimming") == 0) {
fprintf(stderr, "COMPATIBILITY doMerBasedTrimming\n");
if (decodeBoolean("doMerBasedTrimming", val) == 1) {
fprintf(stderr, "COMPATIBILITY doMerBasedTrimming\n");
doTrim_initialNone = 0;
doTrim_initialMerBased = 1;
doTrim_initialFlowBased = 0;
doTrim_initialQualityBased = 0;
doTrim_finalLargestCovered = 1;
doTrim_finalEvidenceBased = 0;
doTrim_finalBestEdge = 0;
}
}
else if (strcasecmp(fea, "doNotQVTrim") == 0) {
fprintf(stderr, "COMPATIBILITY doNotQVTrim\n");
if (decodeBoolean("doNotQVTrim", val) == 1) {
fprintf(stderr, "COMPATIBILITY doNotQVTrim\n");
doTrim_initialNone = 0;
doTrim_initialMerBased = 0;
doTrim_initialFlowBased = 1;
doTrim_initialQualityBased = 0;
doTrim_finalLargestCovered = 0;
doTrim_finalEvidenceBased = 1;
doTrim_finalBestEdge = 0;
}
}
else if (strcasecmp(fea, "goodBadQVThreshold") == 0) {
fprintf(stderr, "COMPATIBILITY doNotOverlapTrim\n");
}
else if (strcasecmp(fea, "doNotOverlapTrim") == 0) {
fprintf(stderr, "COMPATIBILITY doNotOverlapTrim\n");
if (decodeBoolean("doNotOverlapTrim", val) == 1) {
fprintf(stderr, "COMPATIBILITY doNotOverlapTrim\n");
doTrim_initialNone = 0;
doTrim_initialMerBased = 0;
doTrim_initialFlowBased = 0;
doTrim_initialQualityBased = 0;
doTrim_finalLargestCovered = 0;
doTrim_finalEvidenceBased = 0;
doTrim_finalBestEdge = 0;
}
}
else if (strcasecmp(fea, "doConsensusCorrection") == 0)
doConsensusCorrection = decodeBoolean("doConsensusCorrection", val);
// Gatekeeper options
else if (strcasecmp(fea, "forceShortReadFormat") == 0)
forceShortReadFormat = decodeBoolean("forceShortReadFormat", val);
// Illumina options, just to make it not complain about unknown features
else if ((strcasecmp(fea, "illuminaFastQType") == 0) ||
(strcasecmp(fea, "illuminaOrientation") == 0) ||
(strcasecmp(fea, "illuminaQSequence") == 0) ||
(strcasecmp(fea, "illuminaSequence") == 0))
// These are now errors, handled by AS_GKP_illumina.C.
;
else if ((strcasecmp(fea, "fastqQualityValues") == 0) ||
(strcasecmp(fea, "fastqOrientation") == 0) ||
(strcasecmp(fea, "fastqMates") == 0) ||
(strcasecmp(fea, "fastqReads") == 0))
;
// Library options (orientation is not a feature, it's part of the library)
else if (strcasecmp(fea, "constantInsertSize") == 0)
constantInsertSize = decodeBoolean("constantInsertSize", val);
else
fprintf(stderr, "gkLibrary_decodeFeatures()-- found feature '%s' but don't understand it.\n",
fea);
}
errorCode decodeDateTimeValue(EXIStream* strm, EXIType dtType, EXIPDateTime* dt_val)
{
errorCode tmp_err_code = EXIP_UNEXPECTED_ERROR;
Integer year;
unsigned int monDay = 0;
unsigned int timeVal = 0;
boolean presence = FALSE;
dt_val->presenceMask = 0;
DEBUG_MSG(INFO, DEBUG_STREAM_IO, (">> (dateTime)"));
if(dtType == VALUE_TYPE_DATE_TIME || dtType == VALUE_TYPE_DATE || dtType == VALUE_TYPE_YEAR)
{
/* Year component */
TRY(decodeIntegerValue(strm, &year));
dt_val->dateTime.tm_year = (int)year - 100;
}
else
{
dt_val->dateTime.tm_year = INT_MIN;
}
if(dtType == VALUE_TYPE_DATE_TIME || dtType == VALUE_TYPE_DATE || dtType == VALUE_TYPE_MONTH)
{
/* MonthDay component */
TRY(decodeNBitUnsignedInteger(strm, 9, &monDay));
dt_val->dateTime.tm_mon = monDay / 32 - 1;
dt_val->dateTime.tm_mday = monDay % 32;
}
else
{
dt_val->dateTime.tm_mon = INT_MIN;
dt_val->dateTime.tm_mday = INT_MIN;
}
if(dtType == VALUE_TYPE_DATE_TIME || dtType == VALUE_TYPE_TIME)
{
/* Time component */
TRY(decodeNBitUnsignedInteger(strm, 17, &timeVal));
dt_val->dateTime.tm_hour = (timeVal / 64) / 64;
dt_val->dateTime.tm_min = (timeVal / 64) % 64;
dt_val->dateTime.tm_sec = timeVal % 64;
/* FractionalSecs presence component */
TRY(decodeBoolean(strm, &presence));
if(presence)
{
UnsignedInteger fSecs = 0;
unsigned int tmp = 0;
dt_val->presenceMask = dt_val->presenceMask | FRACT_PRESENCE;
dt_val->fSecs.offset = 0;
dt_val->fSecs.value = 0;
/* FractionalSecs component */
TRY(decodeUnsignedInteger(strm, &fSecs));
while(fSecs != 0)
{
tmp = fSecs % 10;
dt_val->fSecs.offset++;
if(tmp != 0)
{
dt_val->fSecs.value = dt_val->fSecs.value*10 + tmp;
}
fSecs = fSecs / 10;
}
dt_val->fSecs.offset -= 1;
}
}
else
{
dt_val->dateTime.tm_hour = INT_MIN;
dt_val->dateTime.tm_min = INT_MIN;
dt_val->dateTime.tm_sec = INT_MIN;
}
/* TimeZone presence component */
TRY(decodeBoolean(strm, &presence));
if(presence)
{
unsigned int tzone = 0;
dt_val->presenceMask = dt_val->presenceMask | TZONE_PRESENCE;
TRY(decodeNBitUnsignedInteger(strm, 11, &tzone));
dt_val->TimeZone = tzone;
}
return EXIP_OK;
}
