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SReport user manual

Creates two types of summary reports in html format

Running the program

Usage C executable (in folder bin):

Usage: ./Sreport -i <INPUT_FOLDER> -t <Q|T|D> -o <OUTPUT_FILE>
Uses all *bin files found in a folder (output of Qreport|trimFilter)
and generates a summary report in html format (of Qreport|trimFilter).
Options:
-v Prints package version.
-h Prints help dialog.
-i Input folder containing *bin data (output from Qreport). Mandatory option.
-t {Q,F,D} Type of report to be generated: 'Q' for quality summary
report, 'F' for filter summary report, and 'D' for double stranded
data filter summary report. Mandatory option,
-o Output file (with NO extension). Mandatory option.

Output description

Example

Option -t Q

An example is given in the folder examples/QReport_Sreport. To run an example, type,

$ cd example/Qreport_Sreport/run_test/
$ ../../../bin/SReport -i ./ -t Q -o my_test_summary_report

and compare it with the provided run example, as specified in the README file under ./examples/QReport_Sreport

NOTE: it has to be run AFTER Qreport example

Option -t F

In folder .examples/trimFilter_Sreport/bin_files, 30 fake ./trimFilter binary output files were generated (with the R script create_fake_bins.R). An html output was created out of them (.examples/trimFilter_Sreport/bin_files/filter_Sreport_example.html). It can be reproduced if you run:

$ ../../bin/Sreport -i .bin_files/ -o ./bin_files/filter_Sreport_new -t F

Option -t D

In folder .examples/trimFilterDS_Sreport/bin_files, 30 fake ./trimFilterDS binary output files were generated (with the R script create_fake_bins.R). An html output was created out of them (.examples/trimFilterDS_Sreport/bin_files/DS_Sreport_example.html). It can be reproduced if you run:

$ ../../bin/Sreport -i .bin_files/ -o ./bin_files/DS_Sreport_new -t F

Contributors

Paula Pérez Rubio

License

GPL v3 (see LICENSE.txt)