public class SAMFileHeader extends AbstractSAMHeaderRecord
Modifier and Type | Class and Description |
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static class |
SAMFileHeader.GroupOrder |
static class |
SAMFileHeader.PgIdGenerator
Little class to generate program group IDs
|
static class |
SAMFileHeader.SortOrder
Ways in which a SAM or BAM may be sorted.
|
Modifier and Type | Field and Description |
---|---|
static Set<String> |
ACCEPTABLE_VERSIONS |
static String |
CURRENT_VERSION |
static String |
GROUP_ORDER_TAG |
static String |
SORT_ORDER_TAG |
static Set<String> |
STANDARD_TAGS
These tags are of known type, so don't need a type field in the text representation.
|
static String |
VERSION_TAG |
serialVersionUID
Constructor and Description |
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SAMFileHeader() |
SAMFileHeader(SAMSequenceDictionary dict)
Constructor that initializes the sequence dictionary with the provided one.
|
attributesEqual, attributesHashCode, getAttribute, getAttributes, getId, setAttribute, setAttribute, toString
public static final String VERSION_TAG
public static final String SORT_ORDER_TAG
public static final String GROUP_ORDER_TAG
public static final String CURRENT_VERSION
public SAMFileHeader()
public SAMFileHeader(SAMSequenceDictionary dict)
public String getVersion()
public String getCreator()
public SAMSequenceDictionary getSequenceDictionary()
public List<SAMReadGroupRecord> getReadGroups()
public SAMSequenceRecord getSequence(String name)
public SAMReadGroupRecord getReadGroup(String name)
public void setSequenceDictionary(SAMSequenceDictionary sequenceDictionary)
public void addSequence(SAMSequenceRecord sequenceRecord)
public SAMSequenceRecord getSequence(int sequenceIndex)
public int getSequenceIndex(String sequenceName)
public void setReadGroups(List<SAMReadGroupRecord> readGroups)
public void addReadGroup(SAMReadGroupRecord readGroup)
public List<SAMProgramRecord> getProgramRecords()
public void addProgramRecord(SAMProgramRecord programRecord)
public SAMProgramRecord getProgramRecord(String pgId)
public void setProgramRecords(List<SAMProgramRecord> programRecords)
programRecords
- This list is used directly, not copied.public SAMProgramRecord createProgramRecord()
public SAMFileHeader.SortOrder getSortOrder()
public void setSortOrder(SAMFileHeader.SortOrder so)
public SAMFileHeader.GroupOrder getGroupOrder()
public void setGroupOrder(SAMFileHeader.GroupOrder go)
public String getTextHeader()
public void setTextHeader(String textHeader)
public void addComment(String comment)
public void setComments(Collection<String> comments)
public List<SAMValidationError> getValidationErrors()
public void addValidationError(SAMValidationError error)
public void setValidationErrors(Collection<SAMValidationError> errors)
public final SAMFileHeader clone()