Mercurial > repos > dawe > srf2fastq
annotate srf2fastq/io_lib-1.12.2/man/man1/illumina2srf.1 @ 0:d901c9f41a6a default tip
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author | dawe |
---|---|
date | Tue, 07 Jun 2011 17:48:05 -0400 |
parents | |
children |
rev | line source |
---|---|
0
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1 .TH illumina2srf 1 "September 29" "" "Staden io_lib" |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3 .SH "NAME" |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
4 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
5 .PP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
6 .BR illumina2srf |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
7 \- Builds an SRF file from an Illumina/Solexa GA run folder. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
8 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
9 .SH "SYNOPSIS" |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
10 .PP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
11 \fBillumina2srf\fR [\fIoptions\fR] \fItile_seq_file\fR ... |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
12 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
13 .SH "DESCRIPTION" |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
14 .PP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
15 \fBillumina2srf\fR converts the Illumina GA-pipeline run folder output |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
16 into an SRF file. It should be run from the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
17 Bustard\fI<version><date>\fR directory. It has a wealth of options, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
18 listed below, although many have defaults and may be ommitted if the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
19 run folder follows the standard directory layout. The arguments, after |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
20 the options, should be the filenames of the sequence files, eg |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
21 \fIs_8_*_seq.txt\fR. All other filenames are derived from the _seq.txt |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
22 filenames. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
23 .PP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
24 The main structure of an SRF file is as a container, much like zip or |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
25 tar. The contents however may be split into variable and common |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
26 components allowing for better compression. For \fBillumina2srf\fR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
27 that means that we store trace data in ZTR format with common ZTR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
28 chunks (text identifiers such as base-caller name and version, matrix |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
29 files and compression specifications) in an SRF \fIData Block |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
30 Header\fR and variable components (sequence, quality and traces) in |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
31 ZTR chunks held within an SRF \fIData Block\fR. Typically we have |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
32 10,000 Data Blocks per Data Block Header. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
33 .PP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
34 The most major decision in producing the SRF file is what data to put |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
35 in it. By default the program writes the sequence and probability |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
36 values along with the "processed" trace intensities. In GAPipeline |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
37 v1.0 and earlier these are in the \fI_seq.txt\fR, \fI_prb.txt\fR and |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
38 \fI_sig2.txt\fR files held within the main Bustard directory. In |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
39 addition to these the \fB-r\fR option requests storage of the "raw" |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
40 trace intensities, comprising both the pre-processed intensities and |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
41 noise estimates from the Firecrest \fI_int.txt\fR and \fI_nse.txt\fR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
42 files respectively. To store only raw intensities, skipping processed |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
43 data, specify the \fB-r -P\fR options. Finally the \fB-I\fR option can |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
44 be used to store data from IPAR format files. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
45 .PP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
46 Confidence values have been a source of large variation over the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
47 pipeline releases. In GAPipeline 1.0 and earlier the \fI_prb.txt\fR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
48 files in the Bustard directory contain four quality values per base |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
49 encoded using a log-odds system: 10*log(P/(1-P)). In addition to this |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
50 there are various calibrated formats in the GERALD directory with one |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
51 Phred scale value per base. See the \fB-qf\fR, \fB-qr\fR and \fB-qc\fR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
52 parameters. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
53 .PP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
54 There are a number of smaller ancillary data files that get stored |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
55 too. As there is no per-lane or per-run storage mechanism in |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
56 these are added for every SRF Data Block Header of which there may be |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
57 several per tile. However the overhead in duplicating this data is not |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
58 significant given the size of the individual SRF Data Blocks. The |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
59 ancillary data files also stored are \fI.params\fR files (for both Bustard |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
60 and Firecrest), matrices (specified using \fB-mf\fR and \fB-mr\fR) and |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
61 phasing XML files (\fB-pf\fR and \fB-pr\fR). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
62 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
63 .SH "OPTIONS" |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
64 .PP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
65 .SS "Trace data-source options" |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
66 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
67 \fB-r\fR, \fB-R\fR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
68 Specifies to store (\fB-r\fR) or not to store (\fB-R\fR - the default) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
69 "raw" data. This is currently comprised of the contents of the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
70 \fI_int.txt\fR and \fI_nse.txt\fR files in the Firecrest directory. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
71 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
72 \fB-p\fR, \fB-P\fR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
73 Specifies to store (\fB-p\fR - the default) or not to store (\fB-P\fR) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
74 the "processed" data. This is the contents of the \fI_sig2.txt\fR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
75 files in the Bustard directory. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
76 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
77 \fB-u\fR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
78 Deprecated. Older GAPipeline releases created \fI_sig.txt\fR files |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
79 holding semi-processed data with compensation for the dye spectral |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
80 overlap, but before phasing correction steps. The \fB-u\fR argument |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
81 indicates that the processed data should be taken from these files |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
82 instead of \fI_sig2.txt\fR. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
83 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
84 \fB-I\fR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
85 Reads \fIIPAR\fR files instead of the raw trace data files. These are |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
86 a different format used by the incremental processing software when |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
87 the pipeline is run on the instrument control PC itself. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
88 .SS "Quality value data-source options" |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
89 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
90 \fB-qf\fR \fIfilename\fR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
91 Specifies the filename of the calibrated quality values for the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
92 forward-read or both the forward and reverse read combined if |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
93 appropriate. \fIfilename\fR should be in Illumina's fastq derivative |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
94 format, with quality values stored as ASCII 64 plus the log-odds |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
95 score. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
96 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
97 \fB-qr\fR \fIfilename\fR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
98 If the calibrated fastq files are split into forward and reverse files |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
99 then \fIfilename\fR specifies the reverse sequences. Otherwise we |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
100 assume they are tacked onto the end of the forward sequences specified |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
101 in \fB-qf\fR. Like the former file, this should be in Illumina's |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
102 fastq-like format. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
103 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
104 \fB-qc\fR \fIdirectory\fR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
105 This is an alternative to the \fB-qf\fR and \fB-qr\fR options above |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
106 and is mutually exclusive with them. This specifies that the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
107 calibrated data should come from files named |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
108 "\fIdirectory\fR/s_%d_qcal.txt" where "%d" is replaced by the current |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
109 tile number. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
110 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
111 .SS "Filtering options" |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
112 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
113 \fB-c\fR \fIvalue\fR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
114 Only store traces that have a "chastity" score >= \fIValue\fR. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
115 This is mutually exclusive with the \fB-C\fR option. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
116 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
117 \fB-C\fR \fIvalue\fR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
118 Until the -c option, traces with a "chastity" score < \fIValue\fR are |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
119 still stored in the SRF file but are marked as bad reads |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
120 instead. \fBsrf2fasta\fR and \fBsrf2fastq\fR have options to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
121 subsequently filter out bad reads using this flag. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
122 This is mutually exclusive with the \fB-c\fR option. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
123 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
124 \fB-s\fR \fIN\fR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
125 This skips the first \fIN\fR cycles of a trace (including signal, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
126 sequence and quality values) when writing it to an SRF file. The |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
127 purpose of this is to remove primer bases, but it is not |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
128 recommended. Instead the SRF file should be using the ZTR region chunk |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
129 (REGN) to indicate which potion of a trace is valid. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
130 .SS "Read naming" |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
131 .PP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
132 Read names are split into two halves, a prefix and a suffix. One |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
133 common prefix is stored in each and every SRF Data Block Header while |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
134 the suffix is stored in every Data Block. This combination allows for |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
135 removal of repetitive data in order to shrink the SRF file size. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
136 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
137 \fB-n\fR \fIformat\fR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
138 .RS |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
139 Controls the format used for creating the sequence name suffix. This |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
140 uses a printf style system of percent expansions that will be replaced |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
141 with the appropriate data. The list of percent expansions are: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
142 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
143 %% |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
144 A literal percent character |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
145 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
146 %d |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
147 Run date (taken from parsing the current working directory) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
148 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
149 %m |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
150 Machine name (taken from parsing the current working directory) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
151 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
152 %r |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
153 Run number (taken from parsing the current working directory) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
154 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
155 %l |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
156 lane number (%L for hexidecimal encoding) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
157 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
158 %t |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
159 tile number (%T for hexidecimal encoding) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
160 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
161 %x |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
162 X coordinate (%X for hexidecimal encoding) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
163 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
164 %y |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
165 Y coordinate (%Y for hexidecimal encoding) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
166 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
167 %c |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
168 Counter; increments by 1 for every sequence in the tile (%C for |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
169 hexidecimal encoding). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
170 .PP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
171 All the above format strings have an optional numerical value between |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
172 the percent and the format character. This is used to control the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
173 field width. For example to print the X and Y coordinates to 3 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
174 hexidecimal places we could use \fB-n "%3X:%3Y"\fR. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
175 .PP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
176 The default format is "\fB%x:%y\fR". |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
177 .RE |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
178 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
179 \fB-N\fR \fIformat\fR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
180 .RS |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
181 Specifies the format string for encoding the reading name prefix. It |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
182 follows the same formatting rules specified in the \fB-n\fR above. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
183 .PP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
184 The default format is "\fB%m_%r:%l:%t:\fR". |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
185 .RE |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
186 .SS "Ancillary data files" |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
187 .PP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
188 These options govern the extra files stored per tile (or strictly |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
189 speaking per SRF Data Block Header). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
190 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
191 \fB-2\fR \fIcycle\fR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
192 This specifies the cycle number, counting from 1, of the second read |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
193 forming a read-pair. It is used for automatic generation of filenames |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
194 in several of the options below and also for construction of the ZTR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
195 region (REGN) chunks. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
196 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
197 \fB-mf\fR \fIfilename\fR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
198 The filename of the forward matrix file. If a single printf numerical |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
199 percent rule is used (such as "%d") then it will be replaced by the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
200 lane number. When not specified the default \fIfilename\fR will be |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
201 \fI../Matrix/s_%d_02_matrix.txt\fR. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
202 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
203 \fB-mr\fR \fIfilename\fR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
204 The filename of the reverse matrix file - only used on paired end |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
205 runs. If a single printf numerical percent rule is used (such as "%d") |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
206 then it will be replaced by the lane number. If a second printf |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
207 percent rule is used then it will be replaced with the cycle number |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
208 that the paired read starts on. This is equivalent to the cycle number |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
209 specified in the \fB-2\fR option plus one. (The plus one comes |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
210 from using the second cycle per end for matrix calibration.) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
211 When \fB-mr\fR is not specified the default \fIfilename\fR will be |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
212 \fI../Matrix/s_%d_%02d_matrix.txt\fR. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
213 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
214 \f-pf\fR \fIfilename\fR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
215 Specifies the filename of the forward-read phasing XML file. As with |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
216 \fR-mf\fR a printf numerical percent rule will be replaced by the lane |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
217 number. The default \fIfilename\fR format is |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
218 \fIPhasing/s_%d_01_phasing.xml\fR. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
219 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
220 \f-pr\fR \fIfilename\fR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
221 Specifies the filename of the reverse-read phasing XML file. As with |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
222 \fR-mr\fR the first two printf numerical percent rules will be |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
223 replaced by the lane number and the cycle number. Unlike \fB-mr\fR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
224 though the cycle number is the value used in the \fB-c\fR option as-is |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
225 instead of plus one. The default \fIfilename\fR format is |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
226 \fIPhasing/s_%d_%02d_phasing.xml\fR. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
227 .SS "Other options" |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
228 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
229 \fB-o\fR \fIsrf_filename\fR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
230 Specifies the output filename to write the SRF data too. Defaults to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
231 "traces.srf". |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
232 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
233 \fB-i\fR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
234 Indicates that an index should be appended to the SRF file. This |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
235 allows for random access based on the sequence name. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
236 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
237 \fB-d\fR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
238 Enable dots-mode. This outputs a full-stop per input tile. Most useful |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
239 in conjunction with quiet mode. Default is off. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
240 .TP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
241 \fB-q\fR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
242 Quiet mode. Do not output commentary on which tile is being processed |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
243 and the metrics about it. Default off. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
244 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
245 .SH "EXAMPLES" |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
246 .PP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
247 To store a lane 4 from a paired end run with raw traces, no |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
248 processed data and calibrated confidence values. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
249 .PP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
250 .nf |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
251 # From Bustard directory |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
252 illumina2srf -o all.srf -r -P \\ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
253 -qf GERALD*/s_4_1_sequence.txt \\ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
254 -qr GERALD*/s_4_2_sequence.txt \\ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
255 s_4_*_seq.txt |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
256 .fi |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
257 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
258 .PP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
259 To store and index only processed traces with chastity >= 0.6 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
260 .PP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
261 .nf |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
262 illumina2srf -o s4.srf -c 0.6 s_4_*_seq.txt |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
263 .fi |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
264 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
265 .SH "CAVEATS" |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
266 .PP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
267 There are many mutually exclusive options, some of which may be for |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
268 processing file formats that no longer exist. This is due to the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
269 history of the program and the rapidly changing nature of the files |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
270 being processed. Some future culling of options and file formats can |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
271 be expected. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
272 .PP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
273 Some assumptions are made as to the directory layout and the ability |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
274 to parse the run folder directory name. There are currently no ways to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
275 override some of this information, including run date, run number and |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
276 GAPipeline program version numbers. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
277 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
278 .SH "AUTHOR" |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
279 .PP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
280 James Bonfield, Wellcome Trust Sanger Institute |