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comparison format_versionning.MD @ 0:a174cbbb12dd draft

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" master branch Updating"
author lain
date Tue, 24 Nov 2020 18:55:08 +0000
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1
2 INTRODUCTION
3 =====
4 This file describes the format of the database generated by XSeeker
5 Preprocessor. This format will evolve in the future to fit users
6 wanted features. That's why there is a history of versions numbers,
7 describing what they brought to the sqlite file, and how it was usefull.
8
9 The first version (the older one) is at the bottom of this file, and the
10 modifications provided by the newest versions are on top of the file.
11
12
13 VERSION 1.1.2
14 =====
15 add missing mz_tab_info$group_length field to produce mzTab
16
17 VERSION 1.1.1
18 =====
19 add missing mz_tab_info$dataset_path field to produce mzTab
20
21
22 VERSION 1.1.0
23 =====
24 Summary:
25 - The field `mz_tab_info` was added in new table smol_xcms_set.
26
27 smol_xcms_set table added
28 -----
29 This table contains a subset of the original ms file.
30
31 mz_tab_info field added to smol_xcms_set
32 -----
33 This field contains five subfields:
34 - sampclass ;
35 - sampnames ;
36 - rtmed ;
37 - mzmed ;
38 - smallmolecule_abundance_assay .
39
40 These fields were added after users asked to export data from XSeeker
41 in mzTab files.
42 XCMS has some functions to extract sampclass, sampnames, rtmed, mzmed
43 and smallmolecule_abundance_assay from xcms set. Then, they are used
44 in the mz tab creation process, but we didn't want to keep the whole
45 xcmsset object. So we used the original code from XCMS and modified it
46 a little bit, justifying the extraction of these new fields.
47
48
49 VERSION 1.0.0
50 =====
51
52
53 DATABASE
54 -----
55
56 ### SAMPLE
57
58 #### RAW
59 This structure is an epurated and enriched version of the original
60 rdata, saved as a compressed env:
61 `blob::blob(fst::compress_fst(serialize(raw, NULL), compression=100))`
62
63 The fields contained in the env are as follow:
64
65 ##### variableMetadata
66
67 ##### tic
68
69 ##### mz
70
71 ##### scanindex
72
73 ##### scantime
74
75 ##### intensity
76
77 ##### polarity
78
79 ##### sample_name
80
81 ##### dataset_path
82
83 ##### process_params
84
85 ##### enriched_rdata
86
87 ##### enriched_rdata_version
88
89 ##### tool_name
90
91 ##### enriched_rdata_doc