bio.std.hts.bam.tagvalue

BAM records may carry arbitrary information in tags.
Value type provides convenient way to work with this information.

Public Imports

std.conv public import std.conv;

Members

Aliases

ArrayElementTagValueTypes alias ArrayElementTagValueTypes = TypeTuple!(CharToType!('c', byte), CharToType!('C', ubyte), CharToType!('s', short), CharToType!('S', ushort), CharToType!('i', int), CharToType!('I', uint), CharToType!('f', float)): Undocumented in source.
PrimitiveTagValueTypes alias PrimitiveTagValueTypes = TypeTuple!(CharToType!('A', char), CharToType!('c', byte), CharToType!('C', ubyte), CharToType!('s', short), CharToType!('S', ushort), CharToType!('i', int), CharToType!('I', uint), CharToType!('f', float)): Undocumented in source.
StringTagValueTypes alias StringTagValueTypes = TypeTuple!(CharToType!('Z', string), CharToType!('H', string)): Undocumented in source.
TypeIdMap alias TypeIdMap = TypeTuple!(TypeId!(char, 0b001_00_1_00), TypeId!(ubyte, 0b001_0_0000), TypeId!(ushort, 0b010_0_0000), TypeId!(uint, 0b100_0__0__0__0__0), TypeId!(byte, 0b001_1_0000), TypeId!(short, 0b010_1_0000), TypeId!(int, 0b100_1_0000), TypeId!(float, 0b100_01_000), TypeId!(ubyte[], 0b001_000_01), TypeId!(ushort[], 0b010_000_01), TypeId!(uint[], 0b100_000_01), TypeId!(byte[], 0b001_100_01), TypeId!(short[], 0b010_100_01), TypeId!(int[], 0b100_100_01), TypeId!(float[], 0b100_01_001), TypeId!(string, 0b001_00_101), TypeId!(string, 0b001_01_101), TypeId!(typeof(null), 0b0000_0010)): Undocumented in source.

Classes

UnknownTagTypeException class UnknownTagTypeException: Thrown in case of unrecognized tag type

Functions

charToSizeof uint charToSizeof(char c): Undocumented in source. Be warned that the author may not have intended to support it.
generateUnion string generateUnion(): Undocumented in source. Be warned that the author may not have intended to support it.
injectOpAssign string injectOpAssign(): Undocumented in source. Be warned that the author may not have intended to support it.
injectOpCast string injectOpCast(): Undocumented in source. Be warned that the author may not have intended to support it.
readValueFromArray Value readValueFromArray(char type, const(ubyte)[] bytes, size_t offset): Undocumented in source. Be warned that the author may not have intended to support it.

Structs

CharToType struct CharToType(char c, T): Undocumented in source.
TypeId struct TypeId(T, ubyte id): Undocumented in source.
Value struct Value: Struct for representing tag values.

Templates

ArrayOf template ArrayOf(T): Undocumented in source.
GetTypeId template GetTypeId(T): Get tag for type T.

Examples

import bio.std.hts.bam.reader, bio.std.hts.bam.tagvalue;
...
auto bam = new BamReader("file.bam");
Value v = bam.reads.front["MD"];
assert(v.is_string);
v = 5;
assert(v.is_signed);     // because 5 is of type int which is signed
assert(v == "5");        // converted to string and then compared
v = "abc";
assert(v.is_string);
v = [1, 2, 3];           // integer and float arrays are supported
assert(v.is_numeric_array);
v = [1.5f, 2.3f, 17.0f]; // double[] arrays must be converted to float[]
assert(v.is_numeric_array);
v = 5.6;
assert(v.is_float);
v = -17;
assert(v.is_signed);

bio.std.hts.bam.tagvalue

Public Imports

Members

Aliases

Classes

Functions

Structs

Templates

Examples

Meta

Source