def value_irs(self):
b = ir.TrueIR()
c = ir.Ref('c')
i = ir.I32(5)
j = ir.I32(7)
st = ir.Str('Hail')
a = ir.Ref('a')
aa = ir.Ref('aa')
da = ir.Ref('da')
v = ir.Ref('v')
s = ir.Ref('s')
t = ir.Ref('t')
call = ir.Ref('call')
collect_sig = ir.AggSignature('Collect', [], None, [hl.tint32])
call_stats_sig = ir.AggSignature('CallStats', [], [hl.tint32],
[hl.tcall])
call_stats_type = hl.tstruct(AC=hl.tarray(hl.tint32),
AF=hl.tarray(hl.tfloat64),
AN=hl.tint32,
homozygote_count=hl.tarray(hl.tint32))
hist_sig = ir.AggSignature('Histogram',
[hl.tfloat64, hl.tfloat64, hl.tint32], None,
[hl.tfloat64])
hist_type = hl.tstruct(bin_edges=hl.tarray(hl.tfloat64),
bin_freq=hl.tarray(hl.tint64),
n_smaller=hl.tint64,
n_larger=hl.tint64)
take_by_sig = ir.AggSignature('TakeBy', [hl.tint32], None,
[hl.tfloat64, hl.tfloat64])
take_by_type = hl.tarray(hl.tfloat64)
value_irs = [
i,
ir.I64(5),
ir.F32(3.14),
ir.F64(3.14),
s,
ir.TrueIR(),
ir.FalseIR(),
ir.Void(),
ir.Cast(i, hl.tfloat64),
ir.NA(hl.tint32),
ir.IsNA(i),
ir.If(b, i, j),
ir.Let('v', i, v),
ir.Ref('x'),
ir.ApplyBinaryOp('+', i, j),
ir.ApplyUnaryOp('-', i),
ir.ApplyComparisonOp('EQ', i, j),
ir.MakeArray([i, ir.NA(hl.tint32), ir.I32(-3)],
hl.tarray(hl.tint32)),
ir.ArrayRef(a, i),
ir.ArrayLen(a),
ir.ArrayRange(ir.I32(0), ir.I32(5), ir.I32(1)),
ir.ArraySort(a, b, False),
ir.ToSet(a),
ir.ToDict(da),
ir.ToArray(a),
ir.LowerBoundOnOrderedCollection(a, i, True),
ir.GroupByKey(da),
ir.ArrayMap(a, 'v', v),
ir.ArrayFilter(a, 'v', v),
ir.ArrayFlatMap(aa, 'v', v),
ir.ArrayFold(a, ir.I32(0), 'x', 'v', v),
ir.ArrayScan(a, ir.I32(0), 'x', 'v', v),
ir.ArrayFor(a, 'v', ir.Void()),
ir.AggFilter(ir.TrueIR(), ir.I32(0)),
ir.AggExplode(ir.ArrayRange(ir.I32(0), ir.I32(2), ir.I32(1)), 'x',
ir.I32(0)),
ir.AggGroupBy(ir.TrueIR(), ir.I32(0)),
ir.ApplyAggOp([ir.I32(0)], [], None, collect_sig,
hl.tarray(hl.tint32)),
ir.ApplyScanOp([ir.I32(0)], [], None, collect_sig,
hl.tarray(hl.tint32)),
ir.ApplyAggOp([ir.F64(-2.11)],
[ir.F64(-5.0),
ir.F64(5.0), ir.I32(100)], None, hist_sig,
hist_type),
ir.ApplyAggOp([call], [], [ir.I32(2)], call_stats_sig,
call_stats_type),
ir.ApplyAggOp([ir.F64(-2.11), ir.F64(-2.11)], [ir.I32(10)], None,
take_by_sig, take_by_type),
ir.InitOp(ir.I32(0), [ir.I32(2)], call_stats_sig),
ir.SeqOp(ir.I32(0), [i], collect_sig),
ir.SeqOp(ir.I32(0), [ir.F64(-2.11), ir.I32(17)], take_by_sig),
ir.Begin([ir.Void()]),
ir.MakeStruct([('x', i)]),
ir.SelectFields(s, ['x', 'z']),
ir.InsertFields(s, [('x', i)]),
ir.GetField(s, 'x'),
ir.MakeTuple([i, b]),
ir.GetTupleElement(t, 1),
ir.StringSlice(st, ir.I32(1), ir.I32(2)),
ir.StringLength(st),
ir.In(2, hl.tfloat64),
ir.Die('mumblefoo', hl.tfloat64),
ir.Apply('&&', b, c),
ir.Apply('toFloat64', i),
ir.Uniroot('x', ir.F64(3.14), ir.F64(-5.0), ir.F64(5.0)),
ir.Literal(hl.tarray(hl.tint32), [1, 2, None]),
]
return value_irs
def value_irs(self):
b = ir.TrueIR()
c = ir.Ref('c')
i = ir.I32(5)
j = ir.I32(7)
a = ir.Ref('a')
st = ir.Ref('st')
aa = ir.Ref('aa')
sta = ir.Ref('sta')
da = ir.Ref('da')
nd = ir.Ref('nd')
v = ir.Ref('v')
s = ir.Ref('s')
t = ir.Ref('t')
call = ir.Ref('call')
table = ir.TableRange(5, 3)
matrix_read = ir.MatrixRead(ir.MatrixNativeReader(
resource('backward_compatability/1.0.0/matrix_table/0.hmt'), None, False),
False, False)
block_matrix_read = ir.BlockMatrixRead(ir.BlockMatrixNativeReader(resource('blockmatrix_example/0')))
value_irs = [
i, ir.I64(5), ir.F32(3.14), ir.F64(3.14), s, ir.TrueIR(), ir.FalseIR(), ir.Void(),
ir.Cast(i, hl.tfloat64),
ir.NA(hl.tint32),
ir.IsNA(i),
ir.If(b, i, j),
ir.Coalesce(i, j),
ir.Let('v', i, v),
ir.Ref('x'),
ir.ApplyBinaryPrimOp('+', i, j),
ir.ApplyUnaryPrimOp('-', i),
ir.ApplyComparisonOp('EQ', i, j),
ir.MakeArray([i, ir.NA(hl.tint32), ir.I32(-3)], hl.tarray(hl.tint32)),
ir.ArrayRef(a, i, ir.Str('foo')),
ir.ArrayLen(a),
ir.ArraySort(ir.ToStream(a), 'l', 'r', ir.ApplyComparisonOp("LT", ir.Ref('l'), ir.Ref('r'))),
ir.ToSet(a),
ir.ToDict(da),
ir.ToArray(a),
ir.CastToArray(ir.NA(hl.tset(hl.tint32))),
ir.MakeNDArray(ir.MakeArray([ir.F64(-1.0), ir.F64(1.0)], hl.tarray(hl.tfloat64)),
ir.MakeTuple([ir.I64(1), ir.I64(2)]),
ir.TrueIR()),
ir.NDArrayShape(nd),
ir.NDArrayReshape(nd, ir.MakeTuple([ir.I64(5)])),
ir.NDArrayRef(nd, [ir.I64(1), ir.I64(2)]),
ir.NDArrayMap(nd, 'v', v),
ir.NDArrayMatMul(nd, nd),
ir.LowerBoundOnOrderedCollection(a, i, True),
ir.GroupByKey(da),
ir.StreamMap(st, 'v', v),
ir.StreamZip([st, st], ['a', 'b'], ir.TrueIR(), 'ExtendNA'),
ir.StreamFilter(st, 'v', v),
ir.StreamFlatMap(sta, 'v', ir.ToStream(v)),
ir.StreamFold(st, ir.I32(0), 'x', 'v', v),
ir.StreamScan(st, ir.I32(0), 'x', 'v', v),
ir.StreamJoinRightDistinct(st, st, ['k'], ['k'], 'l', 'r', ir.I32(1), "left"),
ir.StreamFor(st, 'v', ir.Void()),
ir.AggFilter(ir.TrueIR(), ir.I32(0), False),
ir.AggExplode(ir.StreamRange(ir.I32(0), ir.I32(2), ir.I32(1)), 'x', ir.I32(0), False),
ir.AggGroupBy(ir.TrueIR(), ir.I32(0), False),
ir.AggArrayPerElement(ir.ToArray(ir.StreamRange(ir.I32(0), ir.I32(2), ir.I32(1))), 'x', 'y', ir.I32(0), False),
ir.ApplyAggOp('Collect', [], [ir.I32(0)]),
ir.ApplyScanOp('Collect', [], [ir.I32(0)]),
ir.ApplyAggOp('CallStats', [ir.I32(2)], [call]),
ir.ApplyAggOp('TakeBy', [ir.I32(10)], [ir.F64(-2.11), ir.F64(-2.11)]),
ir.Begin([ir.Void()]),
ir.MakeStruct([('x', i)]),
ir.SelectFields(s, ['x', 'z']),
ir.InsertFields(s, [('x', i)], None),
ir.GetField(s, 'x'),
ir.MakeTuple([i, b]),
ir.GetTupleElement(t, 1),
ir.Die(ir.Str('mumblefoo'), hl.tfloat64),
ir.Apply('land', hl.tbool, b, c),
ir.Apply('toFloat64', hl.tfloat64, i),
ir.Literal(hl.tarray(hl.tint32), [1, 2, None]),
ir.TableCount(table),
ir.TableGetGlobals(table),
ir.TableCollect(ir.TableKeyBy(table, [], False)),
ir.TableToValueApply(table, {'name': 'ForceCountTable'}),
ir.MatrixToValueApply(matrix_read, {'name': 'ForceCountMatrixTable'}),
ir.TableAggregate(table, ir.MakeStruct([('foo', ir.ApplyAggOp('Collect', [], [ir.I32(0)]))])),
ir.TableWrite(table, ir.TableNativeWriter(new_temp_file(), False, True, "fake_codec_spec$$")),
ir.TableWrite(table, ir.TableTextWriter(new_temp_file(), None, True, "concatenated", ",")),
ir.MatrixAggregate(matrix_read, ir.MakeStruct([('foo', ir.ApplyAggOp('Collect', [], [ir.I32(0)]))])),
ir.MatrixWrite(matrix_read, ir.MatrixNativeWriter(new_temp_file(), False, False, "", None, None, None)),
ir.MatrixWrite(matrix_read, ir.MatrixNativeWriter(new_temp_file(), False, False, "",
'[{"start":{"row_idx":0},"end":{"row_idx": 10},"includeStart":true,"includeEnd":false}]',
hl.dtype('array<interval<struct{row_idx:int32}>>'),
'some_file')),
ir.MatrixWrite(matrix_read, ir.MatrixVCFWriter(new_temp_file(), None, ir.ExportType.CONCATENATED, None, False)),
ir.MatrixWrite(matrix_read, ir.MatrixGENWriter(new_temp_file(), 4)),
ir.MatrixWrite(matrix_read, ir.MatrixPLINKWriter(new_temp_file())),
ir.MatrixMultiWrite([matrix_read, matrix_read], ir.MatrixNativeMultiWriter(new_temp_file(), False, False)),
ir.BlockMatrixWrite(block_matrix_read, ir.BlockMatrixNativeWriter('fake.bm', False, False, False)),
ir.LiftMeOut(ir.I32(1)),
ir.BlockMatrixWrite(block_matrix_read, ir.BlockMatrixPersistWriter('x', 'MEMORY_ONLY')),
]
return value_irs
def value_irs(self):
b = ir.TrueIR()
c = ir.Ref('c')
i = ir.I32(5)
j = ir.I32(7)
st = ir.Str('Hail')
a = ir.Ref('a')
aa = ir.Ref('aa')
da = ir.Ref('da')
v = ir.Ref('v')
s = ir.Ref('s')
t = ir.Ref('t')
call = ir.Ref('call')
table = ir.TableRange(5, 3)
matrix_read = ir.MatrixRead(ir.MatrixNativeReader(
resource('backward_compatability/1.0.0/matrix_table/0.hmt')), False, False)
value_irs = [
i, ir.I64(5), ir.F32(3.14), ir.F64(3.14), s, ir.TrueIR(), ir.FalseIR(), ir.Void(),
ir.Cast(i, hl.tfloat64),
ir.NA(hl.tint32),
ir.IsNA(i),
ir.If(b, i, j),
ir.Let('v', i, v),
ir.Ref('x'),
ir.ApplyBinaryOp('+', i, j),
ir.ApplyUnaryOp('-', i),
ir.ApplyComparisonOp('EQ', i, j),
ir.MakeArray([i, ir.NA(hl.tint32), ir.I32(-3)], hl.tarray(hl.tint32)),
ir.ArrayRef(a, i),
ir.ArrayLen(a),
ir.ArrayRange(ir.I32(0), ir.I32(5), ir.I32(1)),
ir.ArraySort(a, b, False),
ir.ToSet(a),
ir.ToDict(da),
ir.ToArray(a),
ir.LowerBoundOnOrderedCollection(a, i, True),
ir.GroupByKey(da),
ir.ArrayMap(a, 'v', v),
ir.ArrayFilter(a, 'v', v),
ir.ArrayFlatMap(aa, 'v', v),
ir.ArrayFold(a, ir.I32(0), 'x', 'v', v),
ir.ArrayScan(a, ir.I32(0), 'x', 'v', v),
ir.ArrayFor(a, 'v', ir.Void()),
ir.AggFilter(ir.TrueIR(), ir.I32(0)),
ir.AggExplode(ir.ArrayRange(ir.I32(0), ir.I32(2), ir.I32(1)), 'x', ir.I32(0)),
ir.AggGroupBy(ir.TrueIR(), ir.I32(0)),
ir.ApplyAggOp('Collect', [], None, [ir.I32(0)]),
ir.ApplyScanOp('Collect', [], None, [ir.I32(0)]),
ir.ApplyAggOp('Histogram', [ir.F64(-5.0), ir.F64(5.0), ir.I32(100)], None, [ir.F64(-2.11)]),
ir.ApplyAggOp('CallStats', [], [ir.I32(2)], [call]),
ir.ApplyAggOp('TakeBy', [ir.I32(10)], None, [ir.F64(-2.11), ir.F64(-2.11)]),
ir.Begin([ir.Void()]),
ir.MakeStruct([('x', i)]),
ir.SelectFields(s, ['x', 'z']),
ir.InsertFields(s, [('x', i)]),
ir.GetField(s, 'x'),
ir.MakeTuple([i, b]),
ir.GetTupleElement(t, 1),
ir.StringSlice(st, ir.I32(1), ir.I32(2)),
ir.StringLength(st),
ir.In(2, hl.tfloat64),
ir.Die(ir.Str('mumblefoo'), hl.tfloat64),
ir.Apply('&&', b, c),
ir.Apply('toFloat64', i),
ir.Uniroot('x', ir.F64(3.14), ir.F64(-5.0), ir.F64(5.0)),
ir.Literal(hl.tarray(hl.tint32), [1, 2, None]),
ir.TableCount(table),
ir.TableGetGlobals(table),
ir.TableCollect(table),
ir.TableAggregate(table, ir.MakeStruct([('foo', ir.ApplyAggOp('Collect', [], None, [ir.I32(0)]))])),
ir.TableWrite(table, new_temp_file(), False, True, "fake_codec_spec$$"),
ir.MatrixAggregate(matrix_read, ir.MakeStruct([('foo', ir.ApplyAggOp('Collect', [], None, [ir.I32(0)]))])),
ir.MatrixWrite(matrix_read, ir.MatrixNativeWriter(new_temp_file(), False, False, "")),
ir.MatrixWrite(matrix_read, ir.MatrixVCFWriter(new_temp_file(), None, False, None)),
ir.MatrixWrite(matrix_read, ir.MatrixGENWriter(new_temp_file(), 4)),
ir.MatrixWrite(matrix_read, ir.MatrixPLINKWriter(new_temp_file())),
]
return value_irs