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lines changed- pasa-plugins
3 files changed
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-3
lines changedSubmodule PASApipeline.wiki updated from e11ec1c to 7840eb9
Submodule transdecoder updated 43 files
- Changelog.txt+14
- PerlLib/Fasta_retriever.pm+53-20
- PerlLib/GFF3_utils2.pm+7-14
- PerlLib/GTF.pm+4.3k
- PerlLib/GTF_utils2.pm+371
- PerlLib/Gene_obj.pm+3-6
- PerlLib/Gene_obj_indexer.pm-75
- PerlLib/Overlap_piler.pm+174
- PerlLib/TiedHash.pm-199
- README-19
- README.md+1-22
- TransDecoder.LongOrfs+9-3
- TransDecoder.Predict+13-5
- __testing/Makefile+36
- __testing/__test.best_w_homology.expected+380
- __testing/__test.simplest.expected+523
- __testing/__test.single_best.expected+381
- __testing/__test.wBlastNPfam.expected+530
- __testing/blastp.outfmt6+76
- __testing/longest_orfs.cds.scores+96
- __testing/longest_orfs.gff3+640
- __testing/pfam.domtblout+239
- sample_data/pasa_example/cleanme.pl+2
- sample_data/pasa_example/runMe.sh+2-2
- sample_data/stringtie_example/cleanme.pl+1
- sample_data/supertranscripts_example/cleanme.pl+1
- sample_data/supertranscripts_example/runMe.sh+4-1
- util/PWM/__deprecated/optimize_atgPWM.pl-148
- util/PWM/__deprecated/optimize_atgPWM_+-.pl-149
- util/PWM/__deprecated/optimize_atgPWM_+-.predict.pl-203
- util/PWM/build_atgPWM_+-.pl+1-1
- util/cdna_alignment_orf_to_genome_orf.pl+2-2
- util/extract_FL_subset.pl-134
- util/gene_list_to_gff.pl+8-7
- util/gff3_file_to_bed.pl+2-2
- util/gff3_file_to_proteins.pl+2-2
- util/gff3_gene_to_gtf_format.pl+65
- util/index_gff3_files_by_isoform.pl-74
- util/nr_ORFs_gff3.pl+2-3
- util/refine_gff3_group_iso_strip_utrs.pl+2-3
- util/remove_eclipsed_ORFs.pl+2-3
- util/select_best_ORFs_per_transcript.pl+9-10
- util/start_codon_refinement.pl+10-4
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