SamFileHeader Class Reference

This class allows a user to get/set the fields in a SAM/BAM Header. More...

#include <SamFileHeader.h>

Collaboration diagram for SamFileHeader:

[legend]

List of all members.

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.
void	addReferenceInfo (const char *referenceSequenceName, int32_t referenceSequenceLength)
	Add reference sequence name and reference sequence length to the header.
void	generateReferenceInfo ()
	Populate the reference info from the SQ fields.
SamStatus::Status	setHeaderFromBamFile (IFILE filePtr)
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.
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* without a trailing "\n".
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.
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/comment 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.
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.

---

Detailed Description

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 35 of file SamFileHeader.h.

---

Member Function Documentation

bool SamFileHeader::addComment

(

const char *

comment

)

Add the specified comment to the header (do not include "@CO" or "\n").

Returns:

true if successfully added, false if not.

Definition at line 223 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. \ returns true if the record was successfully added, false otherwise.

Definition at line 359 of file SamFileHeader.cpp.

{
    // If there is already an HD header or if null
    // was passed in, return false.
    if((myHD != NULL) || (hd == NULL))
    {
        return(false);
    }
    myHD = hd;
   
    myHeaderRecords.push_back(myHD);
    return(true);
}

bool SamFileHeader::addHeaderLine

(

const char *

headerLine

)

Add a header line that is already preformatted in a const char* without a trailing "\n".

Definition at line 208 of file SamFileHeader.cpp.

{
    // Parse the added header line.
    String headerString = headerLine;
    if(parseHeader(headerString))
    {
        // Successfully parsed the header line.
        return(true);
    }
    // Failed to parse the header line, return false.
    return(false);
}

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 192 of file SamFileHeader.cpp.

{
    String headerLine;
    headerLine += "@";
    headerLine += type;
    headerLine += "\t";
    headerLine += tag;
    headerLine += ":";
    headerLine += value;
    return(addHeaderLine(headerLine.c_str()));
}

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. \ returns true if the record was successfully added, false otherwise.

Definition at line 437 of file SamFileHeader.cpp.

References SamHeaderRecord::getTagValue().

{
    // If there is already an PG header, return false.
    if(pg == NULL)
    {
        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.
        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.
    return(false);
}

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. \ returns true if the record was successfully added, false otherwise.

Definition at line 406 of file SamFileHeader.cpp.

References SamHeaderRecord::getTagValue().

{
    if(rg == NULL)
    {
        // null pointer passed in, can't add it.
        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.
        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.
    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. \ returns true if the record was successfully added, false otherwise.

Definition at line 375 of file SamFileHeader.cpp.

References SamHeaderRecord::getTagValue().

{
    if(sq == NULL)
    {
        // null pointer passed in, can't add it.
        return(false);
    }
    const char* name = sq->getTagValue("SN");
    if(strcmp(name, EMPTY_RETURN.c_str()) == 0)
    {
        // SN is not set, so can't add it.
        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);
        return(true);
    }

    // It is already in the hash, so cannot be added.
    return(false);
}

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 633 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.

Returns:

true if successfully set (even if set to "")

Definition at line 120 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 924 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/comment 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 891 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

(

)

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 858 of file SamFileHeader.cpp.

References SamHeaderRecord::isActiveHeaderRecord().

Referenced by generateReferenceInfo(), 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);
}

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 821 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);
}

SamHeaderRecord * SamFileHeader::getNextPGRecord

(

)

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 785 of file SamFileHeader.cpp.

References getNextHeaderRecord(), and SamHeaderRecord::PG.

{
    return(getNextHeaderRecord(myCurrentPGIndex, 
                               SamHeaderRecord::PG));
}

SamHeaderRecord * SamFileHeader::getNextRGRecord

(

)

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 776 of file SamFileHeader.cpp.

References getNextHeaderRecord(), and SamHeaderRecord::RG.

{
    return(getNextHeaderRecord(myCurrentRGIndex, 
                               SamHeaderRecord::RG));
}

SamHeaderRecord * SamFileHeader::getNextSQRecord

(

)

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 767 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 739 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 680 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 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 141 of file SamFileHeader.cpp.

{
    return(myReferenceInfo.getReferenceID(referenceName, addID));
}

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 135 of file SamFileHeader.cpp.

Referenced by SamFile::getNumMappedReadsFromIndex(), SamFile::getNumUnMappedReadsFromIndex(), SamRecord::setMateReferenceName(), and SamRecord::setReferenceName().

{
    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 732 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 664 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 747 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 725 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 646 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.

Returns:

true if successfully removed or did not exist, false if the record still exists.

Definition at line 468 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.

Returns:

true if successfully removed or did not exist, false if the record still exists.

Definition at line 559 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.
        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.

Returns:

true if successfully removed or did not exist, false if the record still exists.

Definition at line 523 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.
        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.

Returns:

true if successfully removed or did not exist, false if the record still exists.

Definition at line 487 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.
        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 937 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 916 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 810 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 802 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 794 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="".

Returns:

true if the tag was successfully set, false if not.

Definition at line 235 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.
            return(false);
        }
        // Succeeded to create the line, add it to the
        // list.
        myHeaderRecords.push_back(myHD);
    }
    return(myHD->setTag(tag, value));
}

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.

Returns:

true if the tag was successfully set, false if not.

Definition at line 326 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.
            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.
            return(false);
        }
    }

    return(pg->setTag(tag, value));
}

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.

Returns:

true if the tag was successfully set, false if not.

Definition at line 291 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.
            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.
            return(false);
        }
    }

    return(rg->setTag(tag, value));
}

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 header is added and so is the SN tag with the value set to the passed in name. The SN tag may not be modified or removed after it is set unless the entire record is deleted.

Returns:

true if the tag was successfully set, false if not.

Definition at line 256 of file SamFileHeader.cpp.

References 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.
        // Add it.
        sq = new SamHeaderSQ();

        if(sq == NULL)
        {
            // Could not create the header record.
            return(false);
        }

        // Created the header record, so add it to the list of SQ lines.
        mySQs.Add(name, sq);
        myHeaderRecords.push_back(sq);

        // Add the key tag 
        if(!sq->addKey(name))
        {
            // Failed to add the key tag, return false.
            return(false);
        }
    }

    return(sq->setTag(tag, value));
}

---

The documentation for this class was generated from the following files:

• bam/SamFileHeader.h
• bam/SamFileHeader.cpp