+ extended documentation
authorFabio <fabio@congo.fml.local>
Mon, 13 Oct 2008 15:39:44 +0000 (17:39 +0200)
committerFabio <fabio@congo.fml.local>
Mon, 13 Oct 2008 15:39:44 +0000 (17:39 +0200)
commit667c4783dd3b59811ead8b79d5dea73b625bb443
treefa4af42ac733f5ebd56f94e773a1ba8a34c9021a
parentdfeb569e210d17b7acdcccdbdab402587659a0b3
+ extended documentation
+ fixed index issues in sequence utils
+ added small example script for splice site score creation
40 files changed:
doc/qpalma-manual.tex
qpalma/DatasetUtils.py
qpalma/Lookup.py
qpalma/OutputFormat.py
test.conf
tests/test_qpalma.py
tests/test_qpalma_installation.py
tests/test_utils.py
tools/calculateAlignmentQuality.m [deleted file]
tools/calculateSizes [deleted file]
tools/data_tools/Makefile [deleted file]
tools/data_tools/datastructures.c [deleted file]
tools/data_tools/datastructures.h [deleted file]
tools/data_tools/debug_tools.c [deleted file]
tools/data_tools/filterReads.c [deleted file]
tools/data_tools/filterReads.py [deleted file]
tools/data_tools/parser.c [deleted file]
tools/data_tools/read.h [deleted file]
tools/data_tools/sort_genes.c [deleted file]
tools/data_tools/tools.c [deleted file]
tools/dataset_scripts/countNotOnChr1-5_pos.py [deleted file]
tools/dataset_scripts/dataStatistic.py [deleted file]
tools/dataset_scripts/mappingInfo.sh [deleted file]
tools/evaluatePrediction.py [deleted file]
tools/extractESTs [deleted file]
tools/plot_param.py [deleted file]
tools/run_specific_scripts/training_dataset/compile_dataset.py [deleted file]
tools/run_specific_scripts/training_dataset/createNewDataset.py [deleted file]
tools/run_specific_scripts/transcriptome_analysis/README [deleted file]
tools/run_specific_scripts/transcriptome_analysis/combine_spliced_map_parts.sh [deleted file]
tools/run_specific_scripts/transcriptome_analysis/compare_predictions/Makefile [deleted file]
tools/run_specific_scripts/transcriptome_analysis/compare_predictions/compare.c [deleted file]
tools/run_specific_scripts/transcriptome_analysis/compare_predictions/gt_test [deleted file]
tools/run_specific_scripts/transcriptome_analysis/compare_predictions/pred_test [deleted file]
tools/run_specific_scripts/transcriptome_analysis/compile_dataset.py [deleted file]
tools/run_specific_scripts/transcriptome_analysis/createExonInfoForGenefinding.py [deleted file]
tools/run_specific_scripts/transcriptome_analysis/createFullMap.sh [deleted file]
tools/run_specific_scripts/transcriptome_analysis/createGenefindingInfo.sh [deleted file]
tools/run_specific_scripts/transcriptome_analysis/createNewDataset.py [deleted file]
tools/spliceScoreConverter.py [new file with mode: 0644]