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libStatGen Software
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libStatGen Software
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This class allows a user to get/set the fields in a SAM/BAM Header. More...
#include <SamFileHeader.h>
Public Member Functions | |
| void | resetHeader () |
| Initialize the header. | |
| int | getReferenceID (const String &referenceName, bool addID=false) |
| Get the reference ID for the specified reference name (chromosome). | |
| int | getReferenceID (const char *referenceName, bool addID=false) |
| Get the reference ID for the specified reference name (chromosome). | |
| const String & | getReferenceLabel (int id) const |
| Return the reference name (chromosome) for the specified reference id. | |
| const SamReferenceInfo & | getReferenceInfo () const |
| Get the Reference Information. | |
| SamReferenceInfo & | getReferenceInfoForBamInterface () |
| int | getNumSQs () |
| Get the number of SQ objects. | |
| int | getNumRGs () |
| Get the number of RG objects. | |
| int | getNumPGs () |
| Get the number of PG objects. | |
| const char * | getSortOrder () |
| Return the Sort Order value that is set in the Header, returning "" if this field does not exist. | |
| const char * | getTagSO () |
| DEPRECATED. | |
| const char * | getErrorMessage () |
| Get the failure message if a method returned failure. | |
Copying a Header | |
These methods are ways of copying the contents of one header into another one. | |
| SamFileHeader (const SamFileHeader &header) | |
| Copy Constructor copies the specified header into this one. | |
| SamFileHeader & | operator= (const SamFileHeader &header) |
| Overload operator = to copy the passed in header into this header. | |
| bool | copy (const SamFileHeader &header) |
| Copy method copies the passed in header into this header. | |
Get the Entire Header | |
Get the entire header as a single string. | |
| bool | getHeaderString (std::string &header) const |
| Set the passed in string to the entire header string, clearing its current contents. | |
Adding an entire header/comment line. | |
These methods are ways of adding an entire header line at once. | |
| bool | addHeaderLine (const char *type, const char *tag, const char *value) |
| Add a header line that is just one tag with a const char* value. | |
| bool | addHeaderLine (const char *headerLine) |
| Add a header line that is already preformatted in a const char*. | |
| bool | addHeader (const char *header) |
| Add a header that is already preformatted in a const char*. | |
| bool | addComment (const char *comment) |
| Add the specified comment to the header (do not include "@CO" or "\n"). | |
Set/Add/Remove a Single Tag | |
The passed in tag should be the two character SAM tag as defined in the SAM spec. A tag is removed from the header record by setting it to "". For the SQ and RG header types, the key tags (SN for SQ and ID for RG) may not be modified or removed once set. This is because these values are used as a lookup key for the header record, so the entire record must be removed. | |
| bool | setHDTag (const char *tag, const char *value) |
| Set the specified tag to the specified value in the HD header, remove the tag by specifying value="". | |
| bool | setSQTag (const char *tag, const char *value, const char *name) |
| Set the specified tag to the specified value in the SQ header with the specified name, remove the tag by specifying value="". | |
| bool | setRGTag (const char *tag, const char *value, const char *id) |
| Set the specified tag to the specified value in the RG header with the specified id, remove the tag by specifying value="". | |
| bool | setPGTag (const char *tag, const char *value, const char *id) |
| Set the specified tag to the specified value in the PG header with the specified id, remove the tag by specifying value="". | |
Add an Already Setup SamHeaderRecord | |
NOTE: These methods add a pointer to the passed in record. The header record will be deleted when it's cleaned up from this header. NOTE: Do NOT delete the passed in record, the SamFileHeader class takes care of that itself. | |
| bool | addHD (SamHeaderHD *hd) |
| Add the HD record to the header. | |
| bool | addSQ (SamHeaderSQ *sq) |
| Add the SQ record to the header. | |
| bool | addRG (SamHeaderRG *rg) |
| Add the RG record to the header. | |
| bool | addPG (SamHeaderPG *pg) |
| Add the PG record to the header. | |
| bool | addRecordCopy (const SamHeaderRecord &hdrRec) |
| Add a copy of the specified header record to the header. | |
Remove an Entire Header Record | |
| bool | removeHD () |
| Remove the HD record. | |
| bool | removeSQ (const char *name) |
| Remove SQ record with the specified key. | |
| bool | removeRG (const char *id) |
| Remove RG record with the specified key. | |
| bool | removePG (const char *id) |
| Remove PG record with the specified key. | |
Get a Specific Tag | |
These methods return the value associated with the specified tag. If the tag does not exist in the record "" is returned. For SQ, RG, and PG the value returned is for the tag associated with the specified key (name/id). If a record with that key does not exist or if the tag does not exist for the record with that key, "" is returned. | |
| const char * | getHDTagValue (const char *tag) |
| Returns the value associated with the specified HD tag, returning "" if the tag does not exist in the header. | |
| const char * | getSQTagValue (const char *tag, const char *name) |
| Get the value associated with the specified tag on the SQ line with the specified sequence name, returning "" if the tag or key does not exist. | |
| const char * | getRGTagValue (const char *tag, const char *id) |
| Get the value associated with the specified tag on the RG line with the specified read group identifier, returning "" if the tag or key does not exist. | |
| const char * | getPGTagValue (const char *tag, const char *id) |
| Get the value associated with the specified tag on the RG line with the specified id, returning "" if the tag or key does not exist. | |
Get a Specific Header Record | |
These methods return a reference to the specific record that was requested, returning NULL if that record does not exist in the header. The returned record can be modified to add/remove some tags. Since a reference is returned, the SamHeaderFile automatically reflects these changes. | |
| SamHeaderHD * | getHD () |
| Get the HD object, returning NULL if there is no HD record. | |
| SamHeaderSQ * | getSQ (const char *name) |
| Get the SQ object with the specified sequence name, returning NULL if there is no SQ object with that key. | |
| SamHeaderRG * | getRG (const char *id) |
| Get the RG object with the specified read group identifier, returning NULL if there is no RG object with that key. | |
| SamHeaderPG * | getPG (const char *id) |
| Get the PG object with the specified id, returning NULL if there is no PG object with that key. | |
Get the Header Record/Comment/Line by Record/Comment/Line | |
These methods iterate through the header. NOTE: both getNextHeaderRecord and getNextHeaderLine increment the same iterator. getNextHeaderRecord that takes a header type uses the same iterator as the getNextXXRecord with that type. Otherwise the iterators are independent. | |
| SamHeaderRecord * | getNextSQRecord () |
| Get the next SQ header record. | |
| SamHeaderRecord * | getNextRGRecord () |
| Get the next RG header record. | |
| SamHeaderRecord * | getNextPGRecord () |
| Get the next PG header record. | |
| void | resetSQRecordIter () |
| Reset to the beginning of the header records so the next call to getNextSQRecord returns the first SQ header record. | |
| void | resetRGRecordIter () |
| Reset to the beginning of the header records so the next call to getNextRGRecord returns the first RG header record. | |
| void | resetPGRecordIter () |
| Reset to the beginning of the header records so the next call to getNextPGRecord returns the first PG header record. | |
| SamHeaderRecord * | getNextHeaderRecord (uint32_t &index, SamHeaderRecord::SamHeaderRecordType headerType) |
| Get the next header record of the specified type starting from the specified index and update the index. | |
| SamHeaderRecord * | getNextHeaderRecord () |
| Get the next header record, but not comment line. | |
| bool | getNextHeaderLine (std::string &headerLine) |
| Set the passed in string to the next header line, overwritting the passed in string. | |
| void | resetHeaderRecordIter () |
| Reset to the beginning of the header records so the next call to getNextHeaderRecord returns the first header line. | |
| void | appendCommentLines (std::string &commentLines) |
| Append all of the comment lines to the specified string. | |
| const char * | getNextComment () |
| Returns the comment on the next comment line. | |
| void | resetCommentIter () |
| Resets to the beginning of the comments so getNextComment returns the first comment. | |
Static Public Attributes | |
| static const std::string | EMPTY_RETURN = "" |
This class allows a user to get/set the fields in a SAM/BAM Header.
Sam/Bam headers contain comments and multiple SamHeaderRecords (HD, SQs, RGs, PGs) comprised of tag/value pairs with each tag only appearing once within a specific record.
Definition at line 34 of file SamFileHeader.h.
| bool SamFileHeader::addComment | ( | const char * | comment | ) |
Add the specified comment to the header (do not include "@CO" or "\n").
Definition at line 213 of file SamFileHeader.cpp.
{
if((comment != NULL) && (strcmp(comment, EMPTY_RETURN.c_str()) != 0))
{
// Valid comment, so add it.
myComments.push_back(comment);
}
return(true);
}
| bool SamFileHeader::addHD | ( | SamHeaderHD * | hd | ) |
Add the HD record to the header.
Note: it adds a pointer to the passed in header record. The header record will be deleted when it is cleaned up from this header.
Definition at line 393 of file SamFileHeader.cpp.
Referenced by addRecordCopy().
{
// If there is already an HD header or if null
// was passed in, return false.
if(myHD != NULL)
{
myErrorMessage = "Failed add an HD tag - there is already one";
return(false);
}
if(hd == NULL)
{
myErrorMessage = "Failed add an HD tag - no tag specified";
return(false);
}
myHD = hd;
myHeaderRecords.push_back(myHD);
return(true);
}
| bool SamFileHeader::addHeader | ( | const char * | header | ) |
Add a header that is already preformatted in a const char*.
Returns true if at least one header line was successfully added.
Definition at line 204 of file SamFileHeader.cpp.
{
// Parse the added header line.
String headerString = header;
return(parseHeader(headerString));
}
| bool SamFileHeader::addHeaderLine | ( | const char * | type, |
| const char * | tag, | ||
| const char * | value | ||
| ) |
Add a header line that is just one tag with a const char* value.
Note: This method will only do one tag per type on a line, so if a type has multiple tags, the whole line needs to be added at once, and a different method should be used.
Definition at line 180 of file SamFileHeader.cpp.
{
String headerLine;
headerLine += "@";
headerLine += type;
headerLine += "\t";
headerLine += tag;
headerLine += ":";
headerLine += value;
return(addHeaderLine(headerLine.c_str()));
}
| bool SamFileHeader::addHeaderLine | ( | const char * | headerLine | ) |
Add a header line that is already preformatted in a const char*.
Returns true if at least one header line was successfully added.
Definition at line 195 of file SamFileHeader.cpp.
{
// Parse the added header line.
String headerString = headerLine;
return(parseHeader(headerString));
}
| bool SamFileHeader::addPG | ( | SamHeaderPG * | pg | ) |
Add the PG record to the header.
Note: it adds a pointer to the passed in header record. The header record will be deleted when it is cleaned up from this header.
Definition at line 492 of file SamFileHeader.cpp.
References SamHeaderRecord::getTagValue().
Referenced by addRecordCopy().
{
// If a null pointer was passed in, return false.
if(pg == NULL)
{
myErrorMessage = "SAM/BAM Header line failed to allocate PG.";
return(false);
}
const char* id = pg->getTagValue("ID");
if(strcmp(id, EMPTY_RETURN.c_str()) == 0)
{
// ID is not set, so can't add the header record.
myErrorMessage = "SAM/BAM Header line failure: Skipping PG line that is missing the ID field.";
return(false);
}
// Determine whether or not a record with this
// key is already in the hash.
if(myPGs.Find(id) < 0)
{
// It is not already in the hash so
// add it.
myPGs.Add(id, pg);
myHeaderRecords.push_back(pg);
return(true);
}
// It is already in the hash, so cannot be added.
myErrorMessage = "SAM/BAM Header line failure: Skipping PG line that has a repeated ID field.";
return(false);
}
| bool SamFileHeader::addRecordCopy | ( | const SamHeaderRecord & | hdrRec | ) |
Add a copy of the specified header record to the header.
Note: it creates a new header record that is identical to the specified one and adds it to the header. The passed in pointer will not be deleted due to this.
Definition at line 526 of file SamFileHeader.cpp.
References addHD(), addPG(), addRG(), addSQ(), SamHeaderRecord::createCopy(), SamHeaderRecord::getType(), SamHeaderRecord::HD, SamHeaderRecord::PG, SamHeaderRecord::RG, and SamHeaderRecord::SQ.
{
SamHeaderRecord* newRec = hdrRec.createCopy();
bool returnVal = true;
switch(newRec->getType())
{
case SamHeaderRecord::HD:
returnVal = addHD((SamHeaderHD*)newRec);
break;
case SamHeaderRecord::PG:
returnVal = addPG((SamHeaderPG*)newRec);
break;
case SamHeaderRecord::RG:
returnVal = addRG((SamHeaderRG*)newRec);
break;
case SamHeaderRecord::SQ:
returnVal = addSQ((SamHeaderSQ*)newRec);
break;
default:
myErrorMessage = "Failed to copy a header record, unknown type.";
returnVal = false;
break;
}
return(returnVal);
}
| bool SamFileHeader::addRG | ( | SamHeaderRG * | rg | ) |
Add the RG record to the header.
Note: it adds a pointer to the passed in header record. The header record will be deleted when it is cleaned up from this header.
Definition at line 458 of file SamFileHeader.cpp.
References SamHeaderRecord::getTagValue().
Referenced by addRecordCopy().
{
if(rg == NULL)
{
// null pointer passed in, can't add it.
myErrorMessage = "SAM/BAM Header line failed to allocate RG.";
return(false);
}
const char* id = rg->getTagValue("ID");
if(strcmp(id, EMPTY_RETURN.c_str()) == 0)
{
// ID is not set, so can't add it.
myErrorMessage = "SAM/BAM Header line failure: Skipping RG line that is missing the ID field.";
return(false);
}
// Determine whether or not a record with this
// key is already in the hash.
if(myRGs.Find(id) < 0)
{
// It is not already in the hash so
// add it.
myRGs.Add(id, rg);
myHeaderRecords.push_back(rg);
return(true);
}
// It is already in the hash, so cannot be added.
myErrorMessage = "SAM/BAM Header line failure: Skipping RG line that has a repeated ID field.";
return(false);
}
| bool SamFileHeader::addSQ | ( | SamHeaderSQ * | sq | ) |
Add the SQ record to the header.
Note: it adds a pointer to the passed in header record. The header record will be deleted when it is cleaned up from this header.
Definition at line 415 of file SamFileHeader.cpp.
References SamReferenceInfo::add(), and SamHeaderRecord::getTagValue().
Referenced by addRecordCopy().
{
if(sq == NULL)
{
// null pointer passed in, can't add it.
myErrorMessage = "SAM/BAM Header line failed to allocate SQ.";
return(false);
}
const char* name = sq->getTagValue("SN");
const char* length = sq->getTagValue("LN");
if(strcmp(name, EMPTY_RETURN.c_str()) == 0)
{
// SN is not set, so can't add it.
myErrorMessage =
"SAM/BAM Header line failure: Skipping SQ line that is missing the SN field.";
return(false);
}
if(strcmp(length, EMPTY_RETURN.c_str()) == 0)
{
// LN is not set, so can't add it.
myErrorMessage =
"SAM/BAM Header line failure: Skipping SQ line that is missing the LN field.";
return(false);
}
// Determine whether or not a record with this
// key is already in the hash.
if(mySQs.Find(name) < 0)
{
// It is not already in the hash so add it.
mySQs.Add(name, sq);
myHeaderRecords.push_back(sq);
myReferenceInfo.add(name, atoi(length));
return(true);
}
// It is already in the hash, so cannot be added.
myErrorMessage = "SAM/BAM Header line failure: Skipping SQ line that has a repeated SN field.";
return(false);
}
| bool SamFileHeader::copy | ( | const SamFileHeader & | header | ) |
Copy method copies the passed in header into this header.
Returns true if at least one header line was successfully copied.
Definition at line 59 of file SamFileHeader.cpp.
References SamReferenceInfo::clear(), getHeaderString(), and resetHeader().
Referenced by operator=(), and SamFileHeader().
{
// Check to see if the passed in value is the same as this.
if(this == &header)
{
return(true);
}
resetHeader();
// Copy the records by getting the other header's header string
// and parsing it.
std::string newString;
bool status = header.getHeaderString(newString);
String newHeaderString = newString.c_str();
status &= parseHeader(newHeaderString);
myCurrentHeaderIndex = header.myCurrentHeaderIndex;
myCurrentCommentIndex = header.myCurrentCommentIndex;
// Clear the reference info and copy it to ensure it is the same.
myReferenceInfo.clear();
// Copy Reference contigs, hash, lengths.
myReferenceInfo = header.myReferenceInfo;
return(status);
}
| const char * SamFileHeader::getHDTagValue | ( | const char * | tag | ) |
Returns the value associated with the specified HD tag, returning "" if the tag does not exist in the header.
Definition at line 683 of file SamFileHeader.cpp.
References SamHeaderRecord::getTagValue().
{
if(myHD == NULL)
{
// return blank since there is no HD type.
return(EMPTY_RETURN.c_str());
}
return(myHD->getTagValue(tag));
}
| bool SamFileHeader::getHeaderString | ( | std::string & | header | ) | const |
Set the passed in string to the entire header string, clearing its current contents.
Definition at line 131 of file SamFileHeader.cpp.
Referenced by copy().
{
header.clear();
// Keep getting header lines until there are no more - false returned.
unsigned int index = 0;
while(getHeaderLine(index, header) != false)
{
++index;
}
return(true);
}
| const char * SamFileHeader::getNextComment | ( | ) |
Returns the comment on the next comment line.
Returns "" if all comment lines have been returned, until resetCommentIter is called.
Definition at line 985 of file SamFileHeader.cpp.
{
if(myCurrentCommentIndex < myComments.size())
{
return(myComments[myCurrentCommentIndex++].c_str());
}
// Already gone through all the comments, return EMPTY_RETURN.c_str().
return(EMPTY_RETURN.c_str());
}
| bool SamFileHeader::getNextHeaderLine | ( | std::string & | headerLine | ) |
Set the passed in string to the next header line, overwritting the passed in string.
If there are no more header lines or there is an error, false is returned and the passed in string is set to "" until a rest is called. NOTE: both getNextHeaderRecord and getNextHeaderLine increment the same iterator.
Definition at line 941 of file SamFileHeader.cpp.
{
headerLine = EMPTY_RETURN.c_str();
// Until the header is set, keep reading.
// Header could return EMPTY_RETURN.c_str() if the header line is blank.
while(headerLine == EMPTY_RETURN.c_str())
{
if(getHeaderLine(myCurrentHeaderIndex, headerLine) == false)
{
// getHeaderLine failed, so stop processing, and return false.
return(false);
}
else
{
// In range, increment the index.
++myCurrentHeaderIndex;
}
}
return(true);
}
| SamHeaderRecord * SamFileHeader::getNextHeaderRecord | ( | uint32_t & | index, |
| SamHeaderRecord::SamHeaderRecordType | headerType | ||
| ) |
Get the next header record of the specified type starting from the specified index and update the index.
After all headers of that type have been retrieved, NULL is returned until a reset is called for that type.
Definition at line 871 of file SamFileHeader.cpp.
References SamHeaderRecord::getType(), and SamHeaderRecord::isActiveHeaderRecord().
{
SamHeaderRecord* foundRecord = NULL;
// Loop until a record is found or until out of range of the
// headerRecord vector.
while((index < myHeaderRecords.size())
&& (foundRecord == NULL))
{
// Get the next record.
foundRecord = myHeaderRecords[index];
// Either way, increment the index.
++index;
// Check to see if the next record is active.
if(!foundRecord->isActiveHeaderRecord())
{
// Not active, so clear the pointer.
foundRecord = NULL;
}
// Check to see if the record is the right type.
else if(foundRecord->getType() != headerType)
{
// Not the right type, so clear the pointer.
foundRecord = NULL;
}
}
// Return the record if it was found. Will be null if none were found.
return(foundRecord);
}
Get the next header record, but not comment line.
After all headers have been retrieved, NULL is returned until a reset is called. NOTE: both getNextHeaderRecord and getNextHeaderLine increment the same iterator.
Definition at line 908 of file SamFileHeader.cpp.
References SamHeaderRecord::isActiveHeaderRecord().
Referenced by getNextPGRecord(), getNextRGRecord(), and getNextSQRecord().
{
// Get the next header record
SamHeaderRecord* foundRecord = NULL;
// Loop until a record is found or until out of range of the
// headerRecord vector.
while((myCurrentHeaderIndex < myHeaderRecords.size())
&& (foundRecord == NULL))
{
// Get the next record.
foundRecord = myHeaderRecords[myCurrentHeaderIndex];
// Either way, increment the index.
++myCurrentHeaderIndex;
// Check to see if the next record is active.
if(!foundRecord->isActiveHeaderRecord())
{
// Not active, so clear the pointer.
foundRecord = NULL;
}
}
// Return the record if it was found. Will be null if none were found.
return(foundRecord);
}
Get the next PG header record.
After all PG headers have been retrieved, NULL is returned until a reset is called. Independent from getNextHeaderRecord, getNextHeaderLine and the other getNextXXRecord methods and the associated reset methods.
Definition at line 835 of file SamFileHeader.cpp.
References getNextHeaderRecord(), and SamHeaderRecord::PG.
{
return(getNextHeaderRecord(myCurrentPGIndex,
SamHeaderRecord::PG));
}
Get the next RG header record.
After all RG headers have been retrieved, NULL is returned until a reset is called. Independent from getNextHeaderRecord, getNextHeaderLine and the other getNextXXRecord methods and the associated reset methods.
Definition at line 826 of file SamFileHeader.cpp.
References getNextHeaderRecord(), and SamHeaderRecord::RG.
{
return(getNextHeaderRecord(myCurrentRGIndex,
SamHeaderRecord::RG));
}
Get the next SQ header record.
After all SQ headers have been retrieved, NULL is returned until a reset is called. Independent from getNextHeaderRecord, getNextHeaderLine and the other getNextXXRecord methods and the associated reset methods.
Definition at line 817 of file SamFileHeader.cpp.
References getNextHeaderRecord(), and SamHeaderRecord::SQ.
{
return(getNextHeaderRecord(myCurrentSQIndex,
SamHeaderRecord::SQ));
}
| SamHeaderPG * SamFileHeader::getPG | ( | const char * | id | ) |
Get the PG object with the specified id, returning NULL if there is no PG object with that key.
Definition at line 789 of file SamFileHeader.cpp.
Referenced by setPGTag().
{
return((SamHeaderPG*)(myPGs.Object(id)));
}
| const char * SamFileHeader::getPGTagValue | ( | const char * | tag, |
| const char * | id | ||
| ) |
Get the value associated with the specified tag on the RG line with the specified id, returning "" if the tag or key does not exist.
Definition at line 730 of file SamFileHeader.cpp.
References SamHeaderRecord::getTagValue().
{
// Look up the id in the hash to get the associated PG object.
SamHeaderPG* pg = (SamHeaderPG*)(myPGs.Object(id));
// If it is NULL - the tag was not found, so return
if(pg == NULL)
{
return(EMPTY_RETURN.c_str());
}
// Found the object, so return the PG Tag.
return(pg->getTagValue(tag));
}
| int SamFileHeader::getReferenceID | ( | const String & | referenceName, |
| bool | addID = false |
||
| ) |
Get the reference ID for the specified reference name (chromosome).
If addID is set to true, a reference id will be created for the referenceName if one does not already exist. If addID is set to false (default), it will return SamReferenceInfo::NO_REF_ID.
Definition at line 146 of file SamFileHeader.cpp.
References SamReferenceInfo::getReferenceID().
Referenced by SamFile::getNumMappedReadsFromIndex(), SamFile::getNumUnMappedReadsFromIndex(), SamRecord::setMateReferenceName(), and SamRecord::setReferenceName().
{
return(myReferenceInfo.getReferenceID(referenceName, addID));
}
| int SamFileHeader::getReferenceID | ( | const char * | referenceName, |
| bool | addID = false |
||
| ) |
Get the reference ID for the specified reference name (chromosome).
If addID is set to true, a reference id will be created for the referenceName if one does not already exist. If addID is set to false (default), it will return SamReferenceInfo::NO_REF_ID.
Definition at line 152 of file SamFileHeader.cpp.
References SamReferenceInfo::getReferenceID().
{
return(myReferenceInfo.getReferenceID(referenceName, addID));
}
| SamHeaderRG * SamFileHeader::getRG | ( | const char * | id | ) |
Get the RG object with the specified read group identifier, returning NULL if there is no RG object with that key.
Definition at line 782 of file SamFileHeader.cpp.
Referenced by setRGTag().
{
return((SamHeaderRG*)(myRGs.Object(id)));
}
| const char * SamFileHeader::getRGTagValue | ( | const char * | tag, |
| const char * | id | ||
| ) |
Get the value associated with the specified tag on the RG line with the specified read group identifier, returning "" if the tag or key does not exist.
Definition at line 714 of file SamFileHeader.cpp.
References SamHeaderRecord::getTagValue().
{
// Look up the id in the hash to get the associated RG object.
SamHeaderRG* rg = (SamHeaderRG*)(myRGs.Object(id));
// If it is NULL - the tag was not found, so return
if(rg == NULL)
{
return(EMPTY_RETURN.c_str());
}
// Found the object, so return the RG Tag.
return(rg->getTagValue(tag));
}
| const char * SamFileHeader::getSortOrder | ( | ) |
Return the Sort Order value that is set in the Header, returning "" if this field does not exist.
Definition at line 797 of file SamFileHeader.cpp.
Referenced by getTagSO().
{
if(myHD == NULL)
{
// No HD, so return blank EMPTY_RETURN.c_str()
return(EMPTY_RETURN.c_str());
}
return(myHD->getSortOrder());
}
| SamHeaderSQ * SamFileHeader::getSQ | ( | const char * | name | ) |
Get the SQ object with the specified sequence name, returning NULL if there is no SQ object with that key.
Definition at line 775 of file SamFileHeader.cpp.
Referenced by SamValidator::isValidRname(), and setSQTag().
{
return((SamHeaderSQ*)(mySQs.Object(name)));
}
| const char * SamFileHeader::getSQTagValue | ( | const char * | tag, |
| const char * | name | ||
| ) |
Get the value associated with the specified tag on the SQ line with the specified sequence name, returning "" if the tag or key does not exist.
Definition at line 696 of file SamFileHeader.cpp.
References SamHeaderRecord::getTagValue().
{
// Look up the name in the hash to get the associated SQ object.
SamHeaderSQ* sq = (SamHeaderSQ*)(mySQs.Object(name));
// If it is NULL - the tag was not found, so return
if(sq == NULL)
{
return(EMPTY_RETURN.c_str());
}
// Found the object, so return the SQ Tag.
return(sq->getTagValue(tag));
}
| bool SamFileHeader::removeHD | ( | ) |
Remove the HD record.
Definition at line 554 of file SamFileHeader.cpp.
References SamHeaderRecord::reset().
{
if(myHD != NULL)
{
// Reset the record. Do not delete it since it is in the headerRecords
// vector and it is not worth the time to remove it from the middle of
// that vector since this is the header and the space does not need
// to be conserved.
myHD->reset();
// Set myHD to null so a new HD could be added.
myHD = NULL;
}
return(true);
}
| bool SamFileHeader::removePG | ( | const char * | id | ) |
Remove PG record with the specified key.
Definition at line 647 of file SamFileHeader.cpp.
References SamHeaderRecord::reset().
{
// Look up the id in the hash.
int hashIndex = myPGs.Find(id);
if(hashIndex < 0)
{
// Not found in the hash, so nothing to
// delete, return true it does not exist
// in the hash.
return(true);
}
// Get the PG.
SamHeaderPG* pg = (SamHeaderPG*)(myPGs.Object(hashIndex));
if(pg == NULL)
{
// pg is null, this is an error since hashIndex was greater than 0,
// so it should have been found.
myErrorMessage = "SAM/BAM Header line failed to get PG object.";
return(false);
}
// Reset the record. Do not delete it since it is in the headerRecords
// vector and it is not worth the time to remove it from the middle of
// that vector since this is the header and the space does not need
// to be conserved.
pg->reset();
// Delete the entry from the hash.
myPGs.Delete(hashIndex);
return(true);
}
| bool SamFileHeader::removeRG | ( | const char * | id | ) |
Remove RG record with the specified key.
Definition at line 610 of file SamFileHeader.cpp.
References SamHeaderRecord::reset().
{
// Look up the id in the hash.
int hashIndex = myRGs.Find(id);
if(hashIndex < 0)
{
// Not found in the hash, so nothing to
// delete, return true it does not exist
// in the hash.
return(true);
}
// Get the RG.
SamHeaderRG* rg = (SamHeaderRG*)(myRGs.Object(hashIndex));
if(rg == NULL)
{
// rg is null, this is an error since hashIndex was greater than 0,
// so it should have been found.
myErrorMessage = "SAM/BAM Header line failed to get RG object.";
return(false);
}
// Reset the record. Do not delete it since it is in the headerRecords
// vector and it is not worth the time to remove it from the middle of
// that vector since this is the header and the space does not need
// to be conserved.
rg->reset();
// Delete the entry from the hash.
myRGs.Delete(hashIndex);
return(true);
}
| bool SamFileHeader::removeSQ | ( | const char * | name | ) |
Remove SQ record with the specified key.
NOTE: Does not remove it from the BAM index.
Definition at line 573 of file SamFileHeader.cpp.
References SamHeaderRecord::reset().
{
// Look up the name in the hash.
int hashIndex = mySQs.Find(name);
if(hashIndex < 0)
{
// Not found in the hash, so nothing to
// delete, return true it does not exist
// in the hash.
return(true);
}
// Get the SQ.
SamHeaderSQ* sq = (SamHeaderSQ*)(mySQs.Object(hashIndex));
if(sq == NULL)
{
// sq is null, this is an error since hashIndex was greater than 0,
// so it should have been found.
myErrorMessage = "SAM/BAM Header line failed to get SQ object.";
return(false);
}
// Reset the record. Do not delete it since it is in the headerRecords
// vector and it is not worth the time to remove it from the middle of
// that vector since this is the header and the space does not need
// to be conserved.
sq->reset();
// Delete the entry from the hash.
mySQs.Delete(hashIndex);
return(true);
}
| void SamFileHeader::resetCommentIter | ( | ) |
Resets to the beginning of the comments so getNextComment returns the first comment.
Definition at line 998 of file SamFileHeader.cpp.
Referenced by resetHeader().
{
myCurrentCommentIndex = 0;
}
| void SamFileHeader::resetHeaderRecordIter | ( | ) |
Reset to the beginning of the header records so the next call to getNextHeaderRecord returns the first header line.
Definition at line 966 of file SamFileHeader.cpp.
Referenced by resetHeader().
{
myCurrentHeaderIndex = 0;
}
| void SamFileHeader::resetPGRecordIter | ( | ) |
Reset to the beginning of the header records so the next call to getNextPGRecord returns the first PG header record.
Definition at line 860 of file SamFileHeader.cpp.
Referenced by resetHeader().
{
myCurrentPGIndex = 0;
}
| void SamFileHeader::resetRGRecordIter | ( | ) |
Reset to the beginning of the header records so the next call to getNextRGRecord returns the first RG header record.
Definition at line 852 of file SamFileHeader.cpp.
Referenced by resetHeader().
{
myCurrentRGIndex = 0;
}
| void SamFileHeader::resetSQRecordIter | ( | ) |
Reset to the beginning of the header records so the next call to getNextSQRecord returns the first SQ header record.
Definition at line 844 of file SamFileHeader.cpp.
Referenced by resetHeader().
{
myCurrentSQIndex = 0;
}
| bool SamFileHeader::setHDTag | ( | const char * | tag, |
| const char * | value | ||
| ) |
Set the specified tag to the specified value in the HD header, remove the tag by specifying value="".
Definition at line 225 of file SamFileHeader.cpp.
References SamHeaderRecord::setTag().
{
if(myHD == NULL)
{
// Need to create the HD line.
myHD = new SamHeaderHD();
if(myHD == NULL)
{
// New failed, return false.
myErrorMessage = "SamFileHeader: Failed to allocate a new HD tag";
return(false);
}
// Succeeded to create the line, add it to the
// list.
myHeaderRecords.push_back(myHD);
}
if(!myHD->setTag(tag, value))
{
myErrorMessage = "SamFileHeader: Failed to set the specified HD tag";
return(false);
}
return(true);
}
| bool SamFileHeader::setPGTag | ( | const char * | tag, |
| const char * | value, | ||
| const char * | id | ||
| ) |
Set the specified tag to the specified value in the PG header with the specified id, remove the tag by specifying value="".
If the header does not yet exist, the header is added and so is the ID tag with the value set to the passed in id. The ID tag may not be modified or removed after it is set unless the entire record is deleted.
Definition at line 353 of file SamFileHeader.cpp.
References SamHeaderRecord::addKey(), getPG(), and SamHeaderRecord::setTag().
{
// Get the PG record for the specified name.
SamHeaderPG* pg = getPG(id);
if(pg == NULL)
{
// The PG does not yet exist.
// Add it.
pg = new SamHeaderPG();
if(pg == NULL)
{
// Could not create the header record.
myErrorMessage = "Failed to allocate a new PG tag";
return(false);
}
// Created the header record, so add it to the list of PG lines.
myPGs.Add(id, pg);
myHeaderRecords.push_back(pg);
// Add the key tag
if(!pg->addKey(id))
{
// Failed to add the key tag, return false.
myErrorMessage = "Failed to add the specified PG key";
return(false);
}
}
if(!pg->setTag(tag, value))
{
myErrorMessage = "Failed to set the specified PG tag";
return(false);
}
return(true);
}
| bool SamFileHeader::setRGTag | ( | const char * | tag, |
| const char * | value, | ||
| const char * | id | ||
| ) |
Set the specified tag to the specified value in the RG header with the specified id, remove the tag by specifying value="".
If the header does not yet exist, the header is added and so is the ID tag with the value set to the passed in id. The ID tag may not be modified or removed after it is set unless the entire record is deleted.
Definition at line 311 of file SamFileHeader.cpp.
References SamHeaderRecord::addKey(), getRG(), and SamHeaderRecord::setTag().
{
// Get the RG record for the specified name.
SamHeaderRG* rg = getRG(id);
if(rg == NULL)
{
// The RG does not yet exist.
// Add it.
rg = new SamHeaderRG();
if(rg == NULL)
{
// Could not create the header record.
myErrorMessage = "Failed to allocate a new RG tag";
return(false);
}
// Created the header record, so add it to the list of RG lines.
myRGs.Add(id, rg);
myHeaderRecords.push_back(rg);
// Add the key tag
if(!rg->addKey(id))
{
// Failed to add the key tag, return false.
myErrorMessage = "Failed to add the specified RG key";
return(false);
}
}
if(!rg->setTag(tag, value))
{
myErrorMessage = "Failed to set the specified RG tag";
return(false);
}
return(true);
}
| bool SamFileHeader::setSQTag | ( | const char * | tag, |
| const char * | value, | ||
| const char * | name | ||
| ) |
Set the specified tag to the specified value in the SQ header with the specified name, remove the tag by specifying value="".
If the header does not yet exist, the tag must be "LN" and the header is added with the specified LN value and the SN value passed in name. The SN & LN tags may not be modified or removed after they are set unless the entire record is deleted.
Definition at line 252 of file SamFileHeader.cpp.
References SamReferenceInfo::add(), SamHeaderRecord::addKey(), getSQ(), and SamHeaderRecord::setTag().
{
// Get the SQ record for the specified name.
SamHeaderSQ* sq = getSQ(name);
if(sq == NULL)
{
// The SQ does not yet exist.
// Make sure the tag is LN.
if(strcmp(tag, "LN") != 0)
{
// LN is required so must be the first tag added
myErrorMessage =
"SamFileHeader:Failed to add the specified SQ key, LN not specified.";
return(false);
}
// Add it.
sq = new SamHeaderSQ();
if(sq == NULL)
{
// Could not create the header record.
myErrorMessage = "SamFileHeader: Failed to allocate a new SQ tag";
return(false);
}
// Created the header record, so add it to the list of SQ lines.
mySQs.Add(name, sq);
myHeaderRecords.push_back(sq);
// value is the length, so update the reference info.
myReferenceInfo.add(name, atoi(value));
// Add the key tag
if(!sq->addKey(name))
{
// Failed to add the key tag, return false.
myErrorMessage = "SamFileHeader:Failed to add the specified SQ key";
return(false);
}
}
else if(strcmp(tag, "LN") == 0)
{
// Cannot modify/remove the LN tag.
myErrorMessage = "SamFileHeader:Cannot modify/remove the SQ's LN tag";
return(false);
}
if(!sq->setTag(tag, value))
{
myErrorMessage = "Failed to set the specified SQ tag";
return(false);
}
return(true);
}
1.7.6.1