Harfang Activity
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ian-d-reid
Activity for Harfang
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Ian Reid committed [c2a572]
Changed invocations of samtools, bgzip, and tabix to lookup executable path
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Removed find_read_islands.py from git
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Moved parse_wigline and trim block from find_read_islands.py to get_model_coverage.py
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Initial implementation of CoverArray class
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Extracted CoverArray definition into coverarray.py
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Replaced uses of coverage tabix files with CoverArray
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Debugged use of np.nditer in get_model_coverage.get_coverblocks
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Implemented remove_untranslatable_CDS.py
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Implemented remove_untranslatable_CDS.py
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Copied gff3-names.py from transcriptomics
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Modified pool_gene_models.py to handle CDS records with no ID
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Cleaned up imports
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Cleaned up imports
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Removed deprecated Bio.Alphabet import from gff3Record.py
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modified gff3Record.get_score to always return a float value
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Removed unused class AugustusConfigParser from run_Harfang.py and moved Augustus_config_parser.py to redundant
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Started implementing test_check_intron_structure.py
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Refactored task_Extract_splice_junctions
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Refactored task_Extract_splice_junctions
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Added completed successfully message to task_Publish_accepted_models
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Fixed --out argument for format_accepted_models in run_Harfang.task_Select_models()
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syntax corrections in run_Harfang:task_Map_reads()
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syntax corrections in run_Harfang:task_Map_reads()
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syntax corrections in run_Harfang:task_Map_reads()
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syntax corrections in run_Harfang:task_Map_reads()
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syntax corrections in run_Harfang:task_Map_reads()
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syntax corrections in run_Harfang:task_Map_reads()
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syntax corrections in run_Harfang:task_Map_reads()
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syntax corrections in run_Harfang:task_Map_reads()
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syntax corrections in run_Harfang:task_Map_reads()
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syntax corrections in run_Harfang:task_Map_reads()
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syntax corrections in run_Harfang:task_Map_reads()
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syntax corrections in run_Harfang:task_Map_reads()
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Corrected STAR config
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Explicitly open files in text mode
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Added test for key presence in run_Harfang:get_args()
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Added format_accepted_models.py
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Added external_predictions to count_contributions_to_final.sh
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Corrected strand names in task_Unhinted_Augustus
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Corrected strand names in task_Unhinted_Augustus
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Removed BAM_hint_dir from file_dep for task_Pool_Models
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Added collect actions to task_Unhinted_Augustus
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Added collect actions to task_Unhinted_Augustus
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Updates to task_Pool_Models and count_contributions_to_final.sh
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Updated script count_contributions_to_final.sh to match filenames in Unhinted_Augustus_Models
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Moved safe_cat to a separate python module
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Broke safe_cat in unsplit_ tasks into slices of 100 filenames
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Corrected and added command logging to task_Complete_Score_Models
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Changed task_Pool_Models to put pooled models in Scored folder
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Fixed translate_ORF_CDS_to_genome.py for transcripts on reverse strand
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Added error messages to startup code
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Extracted prepare function from run_Harfang.run
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Fixed bug in translate_ORF_CDS_to_genome.embed_orfs_in_1_transcript when CDS starts exactly at the start of an internal exon
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Added RM dolumns to extrinsic configuration files
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Corrected Braker option AUGUSTUS_ab_initio
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Corrected Braker option AUGUSTUS_ab_initio
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Added CONFIG checks for Braker etpmode
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Created stub for testGff32predictedTranscriptsAndProteins.py
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Modified run_Harfang.task_Run_Braker to run harfang in etpmode
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Updated output formatting in collect_accepted_models_by_source.py
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Changed value of Braker_gff3 to avoid filename collision in run_Harfang.py
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Modified run_Harfang.py to eliminate score_coverage_homogeneity
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MOdified renumber_models.py to avoid clobbering exon IDs
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Increased MAX_OVERLAP to 50% in merge_strand_representatives.py
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Modified gff32predictedTranscriptsAndProteins.py to handle transcripts with more than one ORF
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Stopped gff3_rename.py from clobbering CDS IDs
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Refactored gff32predictedTranscriptsAndProteins.py
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Added hash and comparison functions to ClassifiedSplice class
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Added check for duplicate splice junctions to avoid spurious retained intron errors in score_models.py
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Corrected sub-version check in Harfang
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added trim_to_exons method to GFF3mRNA
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Fixes to ensure that all GFF3 files comply with SO spec
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Added Unknown to status_precedence dictionary in group_transcripts.py
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Doubled { and } in task_Complete_Score_Models
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Try doubling % in task_make_BAM_hints for compatibility with CmdAction.expand_action
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modified task_make_BAM_hints to yield dictionary literal
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modified task_make_BAM_hints to avoid string formatting error by doit task parser
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Corrected spelling of coverage.wig.gz
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Implemented split_models_at_coverage_gaps.py
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Ian Reid committed [8af8b0]
Added bin/src/depth2wig.py
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Ian Reid committed [561e7f]
Updated README.txt
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Ian Reid committed [8f4d13]
Reolaced gff3Iterator.py and gff3Record.py with latest version from transcriptomics
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Ian Reid committed [d3017e]
Replaced gtftogff3.py with gtf2gff3.py from transcriptomics
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Ian Reid committed [beea17]
Changed run_Harfang.py run() function to accept either cd-hit or cdhit as the executable name (Bug 290)
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Ian Reid committed [5f4843]
Changed run_Harfang.py run() function to ensure that configured values for ProjectDir, Genome, MappedReads, MaskedGenome, and ExternalPredictions are absolute paths (Bug 291)
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Ian Reid committed [adb125]
Changed run_Harfang.py run() function to ensure that configured values for ProjectDir, Genome, MappedReads, MaskedGenome, and ExternalPredictions are absolute paths (Bug 291)
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Ian Reid committed [3eb06e]
Modified mRNA __eq__() to ignore regular exons if CDS records are present (Bug 316)
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Ian Reid committed [fab75d]
Added logging to task_Pool_Augustus_Models for debugging
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Ian Reid committed [2a519d]
Fixed score testing in group_transcripts.py
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Ian Reid committed [c98ce7]
Fixed gene model generation in gff3Iterator
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Ian committed [796012]
Modified src/score_models.check_splice_compatibility to allow exon status to append multiple values
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Modified src/score_models.check_splice_compatibility to allow exon status to append multiple values
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Modified src/score_models.check_splice_compatibility to allow exon status to append multiple values
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Modified src/score_models.check_splice_compatibility to allow exon status to append multiple values
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Ian Reid committed [88437e]
Merged
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Added test to testScore_models.py
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Updated islands2genes.py
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Modified bin/src/gff3Iterator.py to handle null parents
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Modified bin/src/gff3Record.py to handle null parents
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Modified bin/src/gff3Record.py to handle null parents
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