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(parent: ee50e59) | patch
update summary.py to extract data from HiSeq runs.
authorDiane Trout <diane@caltech.edu>
Wed, 16 May 2012 00:36:48 +0000 (17:36 -0700)
committerDiane Trout <diane@caltech.edu>
Wed, 16 May 2012 00:36:48 +0000 (17:36 -0700)
commit96ead161dbfc27002d401bd46139ad7866421b76
treeb2c86dcabff558a9b399fc86fc8b940f73774b44tree | snapshot
parentee50e59d11da2c708ca2c31831f795b147ad35b6commit | diff
update summary.py to extract data from HiSeq runs.
I also commited a much larger swath of hiseq summary files.

One change is Summary and LaneResultSummary now has subclasses to
handle the differences between the GA series and the HiSeq series
runfolders.

At this point the test code is dying trying to read the LaneParameters
out of the gerald config file.
52 files changed:
htsworkflow/pipelines/eland.py diff | blob | history
htsworkflow/pipelines/gerald.py diff | blob | history
htsworkflow/pipelines/summary.py diff | blob | history
htsworkflow/pipelines/test/simulate_runfolder.py diff | blob | history
htsworkflow/pipelines/test/test_runfolder_rta1_12.py diff | blob | history
htsworkflow/pipelines/test/test_summary.py diff | blob | history
htsworkflow/pipelines/test/testdata/1_12/Status.htm [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/Status_Files/ByCycle.htm [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/Status_Files/ByCycle.js [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/Status_Files/ByCycleFrame.htm [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/Status_Files/ByLane.htm [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/Status_Files/ByLane.js [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/Status_Files/Charts.htm [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/Status_Files/Charts.js [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/Status_Files/Controls.htm [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/Status_Files/Controls.js [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/Status_Files/Controls.xsl [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/Status_Files/Error.htm [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/Status_Files/RefreshBtn/r1.png [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/Status_Files/RefreshBtn/r2.png [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/Status_Files/RefreshBtn/r3.png [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/Status_Files/RunInfo.htm [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/Status_Files/RunInfo.xsl [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/Status_Files/RunName.xsl [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/Status_Files/Status.css [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/Status_Files/Status.js [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/Status_Files/StatusError.htm [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/Status_Files/StatusUpdate.xsl [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/Status_Files/Summary.htm [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/Status_Files/Summary.js [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/Status_Files/Summary.xsl [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/Status_Files/TilesPerLane.xsl [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/Status_Files/illumina.png [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/Summary-rta1_12.htm [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/aligned_config_1_12.xml [new file with mode: 0644] blob
htsworkflow/pipelines/test/testdata/1_12/demultiplex_1.12.4.2.xml [new file with mode: 0644] blob
htsworkflow/pipelines/test/testdata/1_12/demultiplexed_bustard_1.12.4.2.xml [new file with mode: 0644] blob
htsworkflow/pipelines/test/testdata/1_12/demultiplexed_summary_1.12.4.2.xml [new file with mode: 0644] blob
htsworkflow/pipelines/test/testdata/1_12/reports/Process Control.png [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/reports/Status.xml [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/reports/StatusUpdate.xml [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/reports/Summary/read1.xml [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/reports/Summary/read2.xml [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/rta_basecalls_config_1.12.4.2.xml [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/1_12/rta_intensities_config_1.12.4.2.xml [new file with mode: 0755] blob
htsworkflow/pipelines/test/testdata/Summary-rta1_12.htm [deleted file] blob | history
htsworkflow/pipelines/test/testdata/aligned_config_1_12.xml [deleted file] blob | history
htsworkflow/pipelines/test/testdata/demultiplex_1.12.4.2.xml [deleted file] blob | history
htsworkflow/pipelines/test/testdata/demultiplexed_bustard_1.12.4.2.xml [deleted file] blob | history
htsworkflow/pipelines/test/testdata/demultiplexed_summary_1.12.4.2.xml [deleted file] blob | history
htsworkflow/pipelines/test/testdata/rta_basecalls_config_1.12.4.2.xml [deleted file] blob | history
htsworkflow/pipelines/test/testdata/rta_intensities_config_1.12.4.2.xml [deleted file] blob | history
htsworkflow sequencing LIMS software