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comparison srf2fastq/io_lib-1.12.2/man/man1/srf_list.1 @ 0:d901c9f41a6a default tip
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author | dawe |
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date | Tue, 07 Jun 2011 17:48:05 -0400 |
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1 .TH srf_list 1 "September 29" "" "Staden io_lib" | |
2 | |
3 .SH "NAME" | |
4 | |
5 .PP | |
6 .BR srf_list | |
7 \- Lists and/or counts the contents of an SRF file | |
8 | |
9 .SH "SYNOPSIS" | |
10 .PP | |
11 \fBsrf_list\fR [\fIoptions\fR] \fIsrf_archive\fR ... | |
12 | |
13 .SH "DESCRIPTION" | |
14 .PP | |
15 \fBsrf_list\fR lists the filenames held within one or more SRF | |
16 container. To simply count the contents rather than list them specify | |
17 the \fB-c\fR option. Note that when in count-only mode if an index is | |
18 present it will be used to determine the number of entries in the | |
19 index and hence sequences in the SRF file. The index cannot be used | |
20 when listing the filenames however as the index itself does not | |
21 contain the full filenames. | |
22 .PP | |
23 Note that it is not possible to count sequences matching certain | |
24 patterns or with specific flags set. \fBsrf_info\fR is a more general | |
25 purpose tool that may cover this. | |
26 | |
27 .SH "OPTIONS" | |
28 .PP | |
29 .TP | |
30 \fB-c\fR | |
31 Counts sequences instead of listing them. Note that this may be | |
32 substantially faster than listing if an index exists. | |
33 .TP | |
34 \fB-v\fR | |
35 Verbose mode. This gives summary count information per file rather | |
36 than just the total at the end. | |
37 .TP | |
38 \fB-l\fR | |
39 Long format. When listing sequence names this also provides | |
40 information on the position in the archive and the size of the | |
41 sequence specific \fIdata block\fR and the size of the shared \fIdata | |
42 block header\fR. | |
43 | |
44 .SH "EXAMPLES" | |
45 .PP | |
46 To count the total number of sequences in several SRF files: | |
47 .PP | |
48 .nf | |
49 srf_list -c *.srf | |
50 .fi | |
51 | |
52 .PP | |
53 To produce a "fofn" (file of filenames) for an SRF file: | |
54 .PP | |
55 .nf | |
56 srf_list foo.srf > foo.fofn | |
57 .fi | |
58 | |
59 .SH "AUTHOR" | |
60 .PP | |
61 James Bonfield, Wellcome Trust Sanger Institute |