1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
|
<?xml version="1.0" encoding="utf-8"?>
<pbds:AlignmentSet
xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd"
xmlns:pbsample="http://pacificbiosciences.com/PacBioSampleInfo.xsd"
xmlns:pbmeta="http://pacificbiosciences.com/PacBioCollectionMetadata.xsd"
xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd"
xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd"
Tags="barcode moreTags mapping mytags"
UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe519c"
TimeStampedName="alignmentset_150304_231155"
MetaType="PacBio.DataSet.AlignmentSet"
Name="Uber alignment set"
Version="2.3.0"
CreatedAt="2015-01-27T09:00:01">
<pbbase:ExternalResources>
<pbbase:ExternalResource
Name="First Alignments BAM"
Description="Points to an example Alignments BAM file."
UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe5293"
TimeStampedName="alignment_bam_150304_231155"
MetaType="PacBio.AlignmentFile.AlignmentBamFile"
ResourceId="file:///mnt/path/to/alignments0.bam" Tags="Example">
<pbbase:FileIndices>
<pbbase:FileIndex
UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe5393"
TimeStampedName="bam_index_150304_231155"
MetaType="PacBio.Index.PacBioIndex"
ResourceId="file:///mnt/path/to/alignments0.pbi"/>
</pbbase:FileIndices>
<pbbase:ExternalResources>
<pbbase:ExternalResource
Name="Reference used to produce BAM file"
Description="Points to the reference used to generate the above BAM file."
UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe5493"
TimeStampedName="reference_fasta_150304_231155"
MetaType="PacBio.ReferenceFile.ReferenceFastaFile"
ResourceId="file:///mnt/path/to/reference.fasta" Tags="Example">
<pbbase:FileIndices>
<pbbase:FileIndex
UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe5593"
TimeStampedName="sawriter_index_150304_231155"
MetaType="PacBio.Index.SaWriterIndex"
ResourceId="file:///mnt/path/to/reference.fasta.sa"/>
<pbbase:FileIndex
UniqueId="b095d0a3-94b8-4918-b3af-a3f81bbe5693"
TimeStampedName="sam_index_150304_231155"
MetaType="PacBio.Index.SamIndex"
ResourceId="file:///mnt/path/to/reference.fasta.fai"/>
</pbbase:FileIndices>
</pbbase:ExternalResource>
</pbbase:ExternalResources>
</pbbase:ExternalResource>
<!-- Is this second BAM necessary? <pbbase:ExternalResource Name="Second Alignments BAM" Description="Points to another example Alignments BAM file, by relative path." MetaType="PacBio.AlignmentFile.AlignmentBamFile" ResourceId="file:./alignments1.bam" Tags="Example">
<pbbase:FileIndices>
<pbbase:FileIndex MetaType="PacBio.Index.PacBioIndex" ResourceId="file:///mnt/path/to/alignments1.pbi"/>
</pbbase:FileIndices>
</pbbase:ExternalResource>-->
</pbbase:ExternalResources>
<!-- START use IDREF here for External Resources, or just duplicate them? <pbds:DataSets>
<pbds:DataSet
UniqueId="ab95d0a3-94b8-4918-b3af-a3f81bbe519c"
TimeStampedName="alignmentset_150304_231155"
MetaType="PacBio.DataSet.AlignmentSet"
Version="2.3.0"
Name="HighQuality Read Alignments">
<pbbase:ExternalResources>
<ExternalResource/>
</pbbase:ExternalResources>
<pbds:Filters> These Filters are in addition to those above. This provides a means to subset and label the parent DataSet further.
<pbds:Filter>
<pbbase:Properties>
<pbbase:Property Name="rq" Value="0.85" Operator=">"/>
</pbbase:Properties>
</pbds:Filter>
</pbds:Filters>
</pbds:DataSet>
<pbds:DataSet
UniqueId="ac95d0a3-94b8-4918-b3af-a3f81bbe519c"
TimeStampedName="alignmentset_150304_231155"
MetaType="PacBio.DataSet.AlignmentSet"
Version="2.3.0"
Name="Alignments to chromosome 1">
<pbbase:ExternalResources>
<ExternalResource/>
</pbbase:ExternalResources>
<pbds:Filters>
<pbds:Filter>
<pbbase:Properties>
<pbbase:Property Name="RNAME" Value="chr1" Operator="=="/>
</pbbase:Properties>
</pbds:Filter>
</pbds:Filters>
</pbds:DataSet>
</pbds:DataSets>
-->
<pbds:DataSetMetadata>
<pbds:TotalLength>50000</pbds:TotalLength>
<pbds:NumRecords>5000</pbds:NumRecords>
<pbds:Provenance CreatedBy="AnalysisJob">
<pbds:ParentTool Name="pbalign" Version="0.1.0" Description="pbalign subreads.dataset.xml reference.dataset.xml"/>
</pbds:Provenance>
</pbds:DataSetMetadata>
</pbds:AlignmentSet>
|
