| 2012-04-13 |
Diane Trout | Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow |
tree | commitdiff |
| 2012-04-12 |
Diane Trout | Extend the adapter id field to support the dual indexed... |
tree | commitdiff |
| 2012-03-27 |
Diane Trout | Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow |
tree | commitdiff |
| 2012-03-26 |
Diane Trout | Switch to lxml for parsing the summary file. |
tree | commitdiff |
| 2012-03-23 |
Diane Trout | Apparently I forgot to remove a parameter why creating... |
tree | commitdiff |
| 2012-03-08 |
Diane Trout | Actually if I provide an output file, I want to write... |
tree | commitdiff |
| 2012-03-07 |
Diane Trout | Forgot to add split attribute to __eq__ test. |
tree | commitdiff |
| 2012-03-06 |
Diane Trout | Support scanning for split fastq files generated by... |
tree | commitdiff |
| 2012-03-06 |
Diane Trout | Add module to convert multiple fastq files into a singl... |
tree | commitdiff |
| 2012-03-05 |
Diane Trout | Use named tuple for sequence flowcell/start/stop/projec... |
tree | commitdiff |
| 2012-03-02 |
Diane Trout | Core functions for saving and finding fastq files gener... |
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| 2012-03-01 |
Diane Trout | Remove some debug prints |
tree | commitdiff |
| 2012-03-01 |
Diane Trout | Simulate a HiSeq runfolder. |
tree | commitdiff |
| 2011-12-20 |
Diane Trout | Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow |
tree | commitdiff |
| 2011-12-20 |
Diane Trout | whitespace reformatting |
tree | commitdiff |
| 2011-12-20 |
Diane Trout | Remove eXecute bit from modules |
tree | commitdiff |
| 2011-11-22 |
Diane Trout | Add a method to override command used to convert srf... |
tree | commitdiff |
| 2011-11-05 |
Diane Trout | Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow |
tree | commitdiff |
| 2011-11-04 |
Diane Trout | Use a logger initialized to the module name much more... |
tree | commitdiff |
| 2011-10-21 |
Diane Trout | Yes generate regular gerald config file. |
tree | commitdiff |
| 2011-10-10 |
Diane Trout | Remove ReadPrep and Thumbnail_Images being generated... |
tree | commitdiff |
| 2011-10-10 |
Diane Trout | Don't need to duplicate %t tile in srf command |
tree | commitdiff |
| 2011-10-06 |
Diane Trout | Add the ability to specify a flowcell id instead of... |
tree | commitdiff |
| 2011-10-04 |
Diane Trout | Add support for flowcells analyzed with Casava 1.7 |
tree | commitdiff |
| 2011-09-19 |
Diane Trout | Output samples that don't have index sequence as well. |
tree | commitdiff |
| 2011-09-19 |
Diane Trout | Python 2.6's DictWriter doesn't have writeheader, so... |
tree | commitdiff |
| 2011-09-17 |
Diane Trout | Add support for tracking the multiplex index sequence. 0.5.4 |
tree | commitdiff |
| 2011-09-12 |
Diane Trout | Add support for first-gen HiSeq flowcells (e.g. ABXX) |
tree | commitdiff |
| 2011-06-30 |
Diane Trout | Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow |
tree | commitdiff |
| 2011-06-23 |
Diane Trout | Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow |
tree | commitdiff |
| 2011-06-22 |
Diane Trout | Move parse_flowcell_id out of frontend.samples.results |
tree | commitdiff |
| 2011-06-11 |
Diane Trout | Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow |
tree | commitdiff |
| 2011-06-11 |
Diane Trout | Convert Rami's DataRun feature to something useful... |
tree | commitdiff |
| 2011-06-10 |
Brandon W. King | The srf/qseq --raw-format patch. |
tree | commitdiff |
| 2011-06-09 |
Diane Trout | Move test srf files to testdata directory so I can... |
tree | commitdiff |
| 2011-06-09 |
Diane Trout | Add a method to return the runfolder name. |
tree | commitdiff |
| 2011-05-26 |
Diane Trout | Merge branch 'add-condition' |
tree | commitdiff |
| 2011-05-09 |
Diane Trout | Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow |
tree | commitdiff |
| 2011-05-09 |
Diane Trout | Report missing directory names to help diagnose sequenc... |
tree | commitdiff |
| 2011-04-18 |
Diane Trout | Be more flexible with fastq filenames. |
tree | commitdiff |
| 2011-02-17 |
Diane Trout | Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow |
tree | commitdiff |
| 2011-02-15 |
Diane Trout | Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow |
tree | commitdiff |
| 2011-02-07 |
Diane Trout | Add in a little bit of qseq2fastq testing code. More... |
tree | commitdiff |
| 2011-02-07 |
Diane Trout | Add documentation about which Phred format we're generating |
tree | commitdiff |
| 2011-02-03 |
Diane Trout | Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow |
tree | commitdiff |
| 2011-01-25 |
Diane Trout | Fix typo in a function name. |
tree | commitdiff |
| 2010-11-01 |
Diane Trout | Only complane about missing genomes if we _wanted_... |
tree | commitdiff |
| 2010-11-01 |
Diane Trout | Check for s_${lane}_02_matrix.txt as well as s_${lane... |
tree | commitdiff |
| 2010-10-27 |
Diane Trout | The WITH_SEQUENCE flag needs to be lower-case "true". |
tree | commitdiff |
| 2010-10-22 |
Diane Trout | Report version number derived from git tag. |
tree | commitdiff |
| 2010-10-19 |
Diane Trout | Set WITH_SEQUENCE as both a per-lane AND global parameter 0.4.5 |
tree | commitdiff |
| 2010-10-08 |
Diane Trout | WITH_SEQUENCE is actually a global GERALD option, remov... |
tree | commitdiff |
| 2010-10-07 |
Diane Trout | Update gerald config file generation. |
tree | commitdiff |
| 2010-09-24 |
Diane Trout | Handle the case when a sequencing lane lacks any yield... |
tree | commitdiff |
| 2010-09-10 |
Diane Trout | Add support for CASAVA 1.7 |
tree | commitdiff |
| 2010-06-10 |
Diane Trout | Extend htsworkflow.pipelines.sequences to also try... |
tree | commitdiff |
| 2010-06-10 |
Diane Trout | Move the code to scan the sequence file archive to... |
tree | commitdiff |
| 2010-06-10 |
Diane Trout | Move the knowledge of the urls for the REST API to... |
tree | commitdiff |
| 2010-04-23 |
Diane Trout | Update summary script to read from the GERALD Summary... |
tree | commitdiff |
| 2010-02-22 |
Diane Trout | there is no such thing as sequence_extended. I was... |
tree | commitdiff |
| 2010-01-21 |
Diane Trout | Update test code to deal with the switch to storing... |
tree | commitdiff |
| 2009-12-11 |
Diane Trout | Modify the srf utility to tar.bz2 the qseq files instea... |
tree | commitdiff |
| 2009-11-10 |
Diane Trout | Don't add the post_run_command unless the option and... |
tree | commitdiff |
| 2009-10-17 |
Diane Trout | Figure out the absolute path to the runfolder for passi... |
tree | commitdiff |
| 2009-10-08 |
Diane Trout | Add the ability not to build srf files. |
tree | commitdiff |
| 2009-10-06 |
Diane Trout | Use eland_extended or eland_pair instead of eland for... |
tree | commitdiff |
| 2009-10-06 |
Diane Trout | Default to sequencing if we don't have a genome for... |
tree | commitdiff |
| 2009-10-02 |
Diane Trout | Test the updated version of extract results that builds... |
tree | commitdiff |
| 2009-09-30 |
Diane Trout | Add building srf files to runfolder as part of --extrac... |
tree | commitdiff |
| 2009-09-26 |
Diane Trout | The config file should also set the SEQUENCE_FORMAT |
tree | commitdiff |
| 2009-09-26 |
Diane Trout | HttpRequest.getcode doesn't exist in python 2.4, use... |
tree | commitdiff |
| 2009-09-26 |
Diane Trout | Implement a client side config file generator. |
tree | commitdiff |
| 2009-09-16 |
Diane Trout | Replace some prints with logging.info messages and |
tree | commitdiff |
| 2009-09-10 |
Diane Trout | Don't crash if there are no lane result summary entries... |
tree | commitdiff |
| 2009-09-10 |
Diane Trout | Report if the Summary.htm file is missing the Lane... |
tree | commitdiff |
| 2009-06-19 |
Diane Trout | I started using ResultLane, so stop treating it like... |
tree | commitdiff |
| 2009-06-17 |
Diane Trout | Add support for extracting data out of Illumina's new... |
tree | commitdiff |
| 2009-06-17 |
Diane Trout | Loading really old run xml files caused the website... |
tree | commitdiff |
| 2009-06-17 |
Diane Trout | remove spurious debug print statements |
tree | commitdiff |
| 2009-05-11 |
Diane Trout | Fix parameter list for base class. |
tree | commitdiff |
| 2009-05-05 |
Diane Trout | Handle lanes that were only sequenced. |
tree | commitdiff |
| 2009-05-05 |
Diane Trout | Return NaN, NaN if a mean +/- deviation value was undef... |
tree | commitdiff |
| 2009-04-24 |
Diane Trout | add --clean option to runfolder |
tree | commitdiff |
| 2009-03-31 |
Diane Trout | Use the image directory name to detect what type of... |
tree | commitdiff |
| 2009-03-31 |
Diane Trout | Don't attempt to save xml for a matrix in firecrest... |
tree | commitdiff |
| 2009-03-31 |
Diane Trout | remove some useless debugging print statements |
tree | commitdiff |
| 2009-03-30 |
Diane Trout | Add unit test to check that the crosstalk matrix was... |
tree | commitdiff |
| 2009-03-30 |
Diane Trout | IPAR detection is more reliable than firecrest so do... |
tree | commitdiff |
| 2009-03-30 |
Diane Trout | Allow specifying a run instead of just scanning the... |
tree | commitdiff |
| 2009-03-28 |
Diane Trout | For pipeline 1.1rc1 or 1.3.2, look for the matrix files... |
tree | commitdiff |
| 2009-03-28 |
Diane Trout | Move sample data from simulate_runfolder into testdata |
tree | commitdiff |
| 2009-03-18 |
Diane Trout | Generate a gerald config file, even if the genome is... |
tree | commitdiff |
| 2009-03-16 |
Diane Trout | Parse runfolders generated with IPAR 1.3 and pipeline... |
tree | commitdiff |
| 2009-03-10 |
Diane Trout | Improve support for eland searching a single fasta... |
tree | commitdiff |
| 2009-02-17 |
Diane Trout | remove cfg_defaults. It was part of an idea I was start... |
tree | commitdiff |
| 2009-02-13 |
Diane Trout | save longer comment describing change |
tree | commitdiff |
| 2009-02-13 |
Diane Trout | Aparently some more recent version of multi eland stopped |
tree | commitdiff |
| 2009-02-13 |
Diane Trout | Merge in the library list, detail, and results download... |
tree | commitdiff |
| 2009-02-12 |
Diane Trout | make our API docstrings more epydoc friendly |
tree | commitdiff |
| 2009-02-12 |
Diane Trout | Add load_pipeline_run_xml, a little function that feeds... |
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