Mercurial > repos > dawe > srf2fastq
annotate srf2fastq/io_lib-1.12.2/man/man1/srf_info.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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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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1 .TH srf_info 1 "September 19" "" "Staden io_lib" |
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2 |
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3 .SH "NAME" |
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4 |
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5 .PP |
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6 .BR srf_info |
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7 \- Lists information about the contents of an SRF file |
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8 |
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9 .SH "SYNOPSIS" |
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10 .PP |
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11 \fBsrf_info\fR [\fI-l\fR bitmap] \fIsrf_archive\fR ... |
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12 |
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13 .SH "DESCRIPTION" |
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14 .PP |
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15 \fBsrf_info\fR lists some simple frequency metrics on the contents of |
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16 an SRF file, both in terms of how many traces there are and the sort of |
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17 data held within them. |
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18 .PP |
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19 For efficiencies sake some control is given over which statistics to |
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20 gather and display. This is controlled by the \fI-l\fR level |
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21 parameter. The value is the summation of one or more of the following |
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22 values, representing the data to display. |
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23 |
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24 .TP |
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25 1 |
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26 Count of good/bad reads. |
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27 .TP |
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28 2 |
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29 Counts and compressed size for selected chunk types. |
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30 .TP |
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31 4 |
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32 Trace count and trace name prefix for each trace_header. |
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33 .TP |
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34 8 |
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35 Base count. |
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36 |
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37 .SH "OPTIONS" |
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38 .PP |
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39 .TP |
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40 \fB-l\fR bitmap |
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41 Controls which statistics to gather and display. Bitmap is a value |
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42 from 0 to 15 (1+2+4+8) as described in the DESCRIPTION section above. |
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43 |
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44 .SH "EXAMPLES" |
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45 .PP |
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46 To count the total number of good and bad reads along with a break |
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47 down of trace names per SRF data-block-header we would use bitmap |
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48 values 1 and 4 combined. |
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49 .PP |
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50 .nf |
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51 srf_info -l 5 foo.srf |
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52 .fi |
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53 |
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54 .PP |
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55 To count the total number of reads for all srf files in a directory. |
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56 .PP |
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57 .nf |
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58 srf_info -l 1 *.srf |
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59 .fi |
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60 |
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61 .SH "AUTHOR" |
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62 .PP |
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63 Steven Leonard, Wellcome Trust Sanger Institute |