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From Genome Analysis Wiki
Jump to navigationJump to search→Retrieving fields from a SAM/BAM Record
| const char* getQuality()
| const char* getQuality()
| Returns the SAM formatted Quality string.
| Returns the SAM formatted Quality string.
|-
| bool getNextSamTag(char* tag, char& vtype, void** value)
| Returns true if a tag was read, false if there are no more tags.
For a true return value, tag is sent to the tag of the tag, vtype is set to the vtype of the tag, and value is a pointer to the value of the tag. You will then need to use a switch to cast value to int, double, char, or String.
|-
| bool isIntegerType(char vtype)
| Returns true if the passed in vtype is of integer ('c', 'C', 's', 'S', 'i', 'I') type.
|-
| bool isDoubleType(char vtype)
| Returns true if the passed in vtype is of double ('f') type.
|-
| bool isCharType(char vtype)
| Returns true if the passed in vtype is of char ('A') type.
|-
| bool isStringType(char vtype)
| Returns true if the passed in vtype is of String ('Z') type.
|-
|-
|-
|}
|}
Example of using getNextSamTag:
<pre>
// record is a previously setup SamRecord.
String recordString = "";
char tag[3];
char vtype;
void* value;
// While there are more tags, write them to the recordString.
while(record.getNextSamTag(tag, vtype, &value) != false)
{
recordString += "\t";
recordString += tag;
recordString += ":";
recordString += vtype;
recordString += ":";
if(record.isIntegerType(vtype))
{
recordString += (int)*(int*)value;
}
else if(record.isDoubleType(vtype))
{
recordString += (double)*(double*)value;
}
else if(record.isCharType(vtype))
{
recordString += (char)*(char*)value;
}
else
{
// String type.
recordString += (String)*(String*)value;
}
}
recordString += "\n";
</pre>
