SamHeader

Represents SAM header

class SamHeader {

enum DEFAULT_FORMAT_VERSION;

this();

this(string header_text);

string format_version;

SortingOrder sorting_order;

SqLineDictionary sequences();

void sequences(SqLineDictionary dict);

RgLineDictionary read_groups;

PgLineDictionary programs;

string[] comments;

int getSequenceIndex(string sequence_name);

SqLine getSequence(size_t index);

string text();

void toString(void delegate(const(char)[]) sink, FormatSpec!char fmt);

void toSam(Sink sink);

void toJson(Sink sink);

void toMsgpack(Packer packer);

}

Constructors

this this(): Construct empty SAM header
this this(string header_text): Parse SAM header given in plain text.

Members

Functions

getSequence SqLine getSequence(size_t index)

getSequenceIndex int getSequenceIndex(string sequence_name)

Zero-based index of sequence. If such sequence does not exist in the header, returns -1.

sequences SqLineDictionary sequences()

Dictionary of @SQ lines. Removal is not allowed, you can only replace the whole dictionary.

sequences void sequences(SqLineDictionary dict)

Undocumented in source. Be warned that the author may not have intended to support it.

text string text()

Get header text representation in SAM format (includes trailing '\n')

toJson void toJson(Sink sink)

Undocumented in source. Be warned that the author may not have intended to support it.

toMsgpack void toMsgpack(Packer packer)

Packs message in the following format:
MsgPack array with elements

format version - string
sorting order - string
@SQ lines - array of dictionaries
@RG lines - array of dictionaries
@PG lines - array of dictionaries

Dictionary keys are the same as in SAM format.

toSam void toSam(Sink sink)

Undocumented in source. Be warned that the author may not have intended to support it.

toString void toString(void delegate(const(char)[]) sink, FormatSpec!char fmt)

Header text representation in SAM ("%s") or JSON format ("%j").
Includes trailing '\n'.

Manifest constants

DEFAULT_FORMAT_VERSION enum DEFAULT_FORMAT_VERSION;

Variables

comments string[] comments;: Array of @CO lines
format_version string format_version;: Format version
programs PgLineDictionary programs;: Dictionary of @PG lines
read_groups RgLineDictionary read_groups;: Dictionary of @RG lines
sorting_order SortingOrder sorting_order;: Sorting order

SamHeader

Constructors

Members

Functions

Manifest constants

Variables

Meta

Source