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commit 5ea6f53dee3e8989b197c60439e32151566d7543 Merge: 5ae7d24 0b7afc2 Author: Michael R. Crusoe <[email protected]> Date: Fri May 20 01:29:38 2016 -0700 Merge tag 'upstream/2.2.0+dfsg' Upstream version 2.2.0+dfsg Analysis/DifferentialExpression/PtR | 80 +- Analysis/DifferentialExpression/ROKU.pl | 2 +- .../TissueEnrichment/DE_graph_to_dot.pl | 55 + .../DE_results_to_pairwise_summary.pl | 160 +++ .../TissueEnrichment/README.md | 5 + .../pairwise_DE_summary_to_DE_classification.pl | 299 ++++++ .../DifferentialExpression/analyze_diff_expr.pl | 8 +- .../cluster_sample_data/cleanme.pl | 2 +- .../cut_tree_into_clusters.pl | 2 +- .../define_clusters_by_cutting_tree.pl | 9 +- .../diff_expr_analysis_to_heatmap_html.pl | 4 +- Analysis/DifferentialExpression/diff_express.cgi | 2 +- .../extract_GO_enriched_genes.pl | 2 +- .../get_transcript_lengths.pl | 2 +- Analysis/DifferentialExpression/merge_matrices.pl | 12 +- .../remove_batch_effects_from_count_matrix.pl | 2 +- .../replicates_to_sample_averages_matrix.pl | 2 +- Analysis/DifferentialExpression/run_DE_analysis.pl | 10 +- Analysis/DifferentialExpression/run_GOseq.pl | 2 +- .../run_TMM_normalization_write_FPKM_matrix.pl | 4 +- .../stratify_diff_expression.pl | 2 +- .../subcluster_to_canvasXpress_html.pl | 2 +- .../FL_trans_analysis_pipeline.pl | 4 +- .../FL_reconstruction_analysis/compute_oracle.pl | 2 +- .../tier_gene_trans_alignments.pl | 4 +- .../util/blat_full_length_mappings.pl | 2 +- .../util/blat_top_tier_genes.pl | 2 +- Butterfly/src/src/TransAssembly_allProbPaths.java | 144 ++- Release.Notes => Changelog.txt | 95 +- Chrysalis/MakeDepend.cc | 2 +- Chrysalis/Makefile | 10 +- Chrysalis/analysis/TranscriptomeGraph.cc | 2 +- Inchworm/src/IRKE.cpp | 122 +-- Inchworm/src/fastaToKmerCoverageStats.cpp | 11 +- PerlLib/Fastq_reader.pm | 17 +- PerlLib/test_htc_gridrunner_LSF.pl | 4 +- PerlLib/test_htc_gridrunner_SGE.pl | 4 +- README | 2 +- README.md | 2 +- Trinity | 47 +- .../test_GraphFromFasta/runMe.sh | 1 + sample_data/test_DE_analysis/Makefile | 6 +- .../test_GOSeq_trinotate_pipe/Spombe/cleanme.pl | 2 +- .../test_GOSeq_trinotate_pipe/Spombe/runMe.sh | 1 + sample_data/test_GenomeGuidedTrinity/cleanme.pl | 2 +- .../test_InSilicoReadNormalization/Makefile | 1 + .../test_InSilicoReadNormalization/cleanme.pl | 10 +- .../test_PE_normalization.mult_read_sets.sh | 11 + sample_data/test_Inchworm/runMe_MPI.sh | 1 + .../test_TissueSpecificityGraph/DE_results.tar.gz | Bin 0 -> 37622593 bytes sample_data/test_TissueSpecificityGraph/Makefile | 10 + .../transcripts.TMM.fpkm.avg_reps.matrix.gz | Bin 0 -> 3467094 bytes sample_data/test_Trinity_Assembly/Makefile | 14 +- .../align_reads_via_bowtie.sh | 3 +- .../__indiv_ex_sample_derived/ex05/runMe.clean.sh | 1 + .../__indiv_ex_sample_derived/ex05/runMe.sh | 1 + .../__indiv_ex_sample_derived/ex09/runMe.sh | 1 + sample_data/test_Trinity_Assembly/cleanme.pl | 4 +- .../misc_run_tests/__runMe_include_long_reads.sh | 2 +- sample_data/test_Trinity_Assembly/runMe.sh | 2 +- .../test_align_and_estimate_abundance/Makefile | 19 +- .../PAIRED_END_ABUNDANCE_ESTIMATION/Makefile | 41 + .../cleanme.pl | 22 +- .../misc_tests/drosoph_denovo.samples.txt | 6 + .../misc_tests/drosoph_ref.samples.txt | 6 + .../misc_tests/mouse_denovo.samples.txt | 6 + .../misc_tests/mouse_ref.samples.txt | 6 + .../misc_tests/schizo_denovo.samples.txt | 6 + .../misc_tests/schizo_ref.samples.txt | 6 + .../misc_tests/test_Drosoph_denovo.sh | 1 + .../misc_tests/test_Drosoph_ref.sh | 1 + .../misc_tests/test_Mouse_denovo.sh | 1 + .../misc_tests/test_Mouse_ref.sh | 1 + .../misc_tests/test_Schizo_denovo.sh | 1 + .../misc_tests/test_Schizo_ref.sh | 1 + .../PAIRED_END_ABUNDANCE_ESTIMATION/samples.txt | 8 + .../SINGLE_END_ABUNDANCE_ESTIMATION/Makefile | 41 + .../cleanme.pl | 23 +- .../misc_tests/drosoph_denovo.samples.txt | 5 + .../misc_tests/drosoph_ref.samples.txt | 6 + .../misc_tests/mouse_denovo.samples.txt | 6 + .../misc_tests/mouse_ref.samples.txt | 6 + .../misc_tests/schizo_denovo.samples.txt | 6 + .../misc_tests/schizo_ref.samples.txt | 6 + .../misc_tests/test_Drosoph_denovo.sh | 1 + .../misc_tests/test_Drosoph_ref.sh | 1 + .../misc_tests/test_Mouse_denovo.sh | 1 + .../misc_tests/test_Mouse_ref.sh | 1 + .../misc_tests/test_Schizo_denovo.sh | 1 + .../misc_tests/test_Schizo_ref.sh | 1 + .../SINGLE_END_ABUNDANCE_ESTIMATION/samples.txt | 8 + .../align_and_estimate_tester.pl | 68 +- .../pairs.Rscript | 6 + .../test_align_and_estimate_abundance/samples.txt | 4 - sample_data/test_full_edgeR_pipeline/cleanme.pl | 2 +- trinity-plugins/Makefile | 10 +- .../fstrozzi-Fastool-7c3e034f05/Makefile | 5 +- trinity-plugins/scaffold_iworm_contigs/Makefile | 4 +- trinity-plugins/slclust/src/Makefile | 21 +- util/SAM_nameSorted_to_uniq_count_stats.pl | 12 +- util/TrinityStats.pl | 2 +- util/abundance_estimates_to_matrix.pl | 84 +- util/align_and_estimate_abundance.pl | 344 ++++--- util/analyze_blastPlus_topHit_coverage.pl | 2 +- util/bowtie_PE_separate_then_join.pl | 6 +- util/fasta_tool | 1054 +++++++++++++++++++- util/filter_low_expr_transcripts.pl | 286 ++++++ util/insilico_read_normalization.pl | 13 +- util/misc/Artemis/join_multi_wig_to_graph_plot.pl | 2 +- util/misc/BLAT_to_SAM.pl | 6 +- util/misc/ButterflyFastaToGraphDot.pl | 2 +- util/misc/HiCpipe_nameSortedSam_to_raw.pl | 2 +- util/misc/Monarch | 2 +- util/misc/N50.pl | 2 +- .../misc/SAM_coordsorted_max_reads_per_position.pl | 2 +- util/misc/SAM_intron_extractor.pl | 2 +- util/misc/SAM_pair_to_bed.pl | 2 +- util/misc/SAM_sortAny_to_count_stats.pl | 2 +- util/misc/SAM_toString.pl | 2 +- util/misc/SAM_to_bed.pl | 2 +- util/misc/SAM_to_fasta.pl | 2 +- util/misc/TophatCufflinksWrapper.pl | 2 +- util/misc/allele_simulator.pl | 2 +- util/misc/average.pl | 2 +- .../extract_bam_reads_per_target_gene.pl | 2 +- .../extract_bam_reads_per_target_transcript.pl | 2 +- util/misc/bam_gene_tests/write_trin_cmds.pl | 2 +- util/misc/blast_outfmt6_group_segments.pl | 2 +- ..._outfmt6_group_segments.to_Markov_Clustering.pl | 2 +- util/misc/blat_util/blat_sam_add_reads2.pl | 2 +- util/misc/blat_util/blat_to_sam.pl | 4 +- util/misc/blat_util/process_BLAT_alignments.pl | 4 +- util/misc/blat_util/top_blat_sam_extractor.pl | 2 +- util/misc/capture_orig_n_unmapped_reads.pl | 2 +- util/misc/cdna_fasta_file_to_transcript_gtf.pl | 2 +- util/misc/check_fastQ_pair_ordering.pl | 2 +- util/misc/contig_ExN50_statistic.pl | 15 +- util/misc/extract_fastQ_pairings.pl | 2 +- util/misc/fastQ_rand_subset.pl | 2 +- ..._subset.reservoir_sampling_reqiures_high_mem.pl | 2 +- util/misc/fasta_file_reformatter.pl | 2 +- util/misc/fasta_filter_by_min_length.pl | 2 +- util/misc/fasta_seq_length.pl | 25 + util/misc/fasta_to_cmd_generator.pl | 2 +- util/misc/fasta_write_sense_n_anti.pl | 2 +- util/misc/fastq_interleave_pairs.pl | 2 +- util/misc/fastq_unweave_pairs.pl | 2 +- util/misc/gene_gff3_to_introns.pl | 2 +- .../get_longest_isoform_seq_per_trinity_gene.pl | 2 +- util/misc/gff3_file_to_cdna.pl | 2 +- util/misc/gff3_file_utr_coverage_trimmer.pl | 2 +- ...f3_to_genome_feature_base_encoding.parse_SAM.pl | 2 +- util/misc/gff3_to_genome_feature_base_encoding.pl | 2 +- util/misc/gmap_gff3_chimera_jaccard_analyzer.pl | 2 +- util/misc/gmap_gff3_to_percent_length_stats.pl | 2 +- util/misc/gmap_native_to_format_converter.pl | 2 +- util/misc/gtf_to_bed_format.pl | 2 +- util/misc/gtf_to_introns.pl | 2 +- util/misc/identify_distal_isoform_variations.pl | 2 +- util/misc/illustrate_ref_comparison.pl | 2 +- util/misc/jaccard_sam_pair_refiner.pl | 2 +- util/misc/kmer_counter.pl | 2 +- util/misc/m8_blastclust.pl | 2 +- util/misc/map_gtf_transcripts_to_genome_annots.pl | 2 +- util/misc/merge_blast_n_rsem_results.pl | 2 +- util/misc/nameSorted_SAM_to_FastQ.pl | 2 +- util/misc/pairwise_kmer_content_comparer.pl | 2 +- util/misc/plot_ExN50_statistic.Rscript | 14 + util/misc/plot_expressed_gene_dist.pl | 2 +- util/misc/print_kmers.pl | 2 +- util/misc/prop_pair_sam_refiner.pl | 2 +- util/misc/run_GSNAP.pl | 27 +- util/misc/run_HISAT.pl | 2 +- util/misc/run_HiCpipe_bowtie.pl | 4 +- util/misc/run_bowtie2.pl | 39 + util/misc/run_read_simulator_per_fasta_entry.pl | 4 +- util/misc/run_read_simulator_per_gene.pl | 2 +- util/misc/run_trimmomatic_qual_trimming.pl | 4 +- util/misc/simulate_illuminaPE_from_transcripts.pl | 2 +- util/misc/simulate_reads_sam_and_fa.pl | 4 +- util/misc/sixFrameTranslation.pl | 2 +- util/misc/sort_fastq.pl | 2 +- .../assess_intron_path_sensitivity.pl | 2 +- util/misc/strip_fasta_header.pl | 2 +- util/misc/transcript_coverage_UTR_trimmer.pl | 4 +- util/misc/transcript_fasta_to_ORF_pics.pl | 2 +- util/misc/transcript_gff3_to_bed.pl | 2 +- util/misc/trinity_component_distribution.pl | 2 +- util/run_DE_analysis_from_samples_file.pl | 2 +- util/run_RSEM_from_samples_file.pl | 2 +- util/run_Trinity_edgeR_pipeline.pl | 22 +- util/run_Trinity_from_samples_file.pl | 2 +- ...AM_coordSorted_fragment_Read_coverage_writer.pl | 2 +- .../SAM_coordSorted_fragment_coverage_writer2.pl | 2 +- .../SAM_extract_properly_mapped_pairs.pl | 2 +- .../SAM_extract_uniquely_mapped_reads.pl | 2 +- .../SAM_filter_out_unmapped_reads.pl | 2 +- util/support_scripts/SAM_ordered_pair_jaccard.pl | 2 +- .../SAM_set_transcribed_orient_info.pl | 2 +- util/support_scripts/SAM_strand_separator.pl | 2 +- util/support_scripts/SAM_to_frag_coords.pl | 2 +- .../define_SAM_coverage_partitions2.pl | 2 +- util/support_scripts/define_coverage_partitions.pl | 2 +- .../support_scripts/extract_reads_per_partition.pl | 2 +- util/support_scripts/fastQ_to_fastA.pl | 2 +- util/support_scripts/fasta_to_tab.pl | 2 +- util/support_scripts/fragment_coverage_writer.pl | 2 +- .../inchworm_transcript_splitter.pl | 2 +- util/support_scripts/jaccard_fasta_clipper.pl | 2 +- util/support_scripts/jaccard_wig_clipper.pl | 2 +- .../merge_left_right_nameSorted_SAMs.pl | 2 +- .../support_scripts/nbkc_merge_left_right_stats.pl | 4 + .../ordered_fragment_coords_to_jaccard.pl | 2 +- ...aseq_alignments_for_genome_assisted_assembly.pl | 2 +- util/support_scripts/run_TMM_scale_matrix.pl | 4 +- .../run_UpperQuartileNormalization_matrix.pl | 8 +- .../salmon_trans_to_gene_results.pl | 165 +++ util/support_scripts/tests/sample_data_tests.py | 56 ++ util/support_scripts/tests/test.py | 187 ---- util/support_scripts/tests/test_prep.py | 55 +- util/support_scripts/tests/tests.py | 34 +- .../write_partitioned_trinity_cmds.pl | 2 +- 222 files changed, 3447 insertions(+), 811 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/trinityrnaseq.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
