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ChangeLog
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1.0.2 (June 18 2019)
-Update util/samtools for Ubuntu 16.04LTS and samtools-1.7
-Fix Perl syntax bug in Circleator::SeqFunction::BAMCoverage [Issue #38]
-Add Ubuntu-based Docker image with Circleator preinstalled.
-Account for additional whitespace differences between SVG 2.59 and 2.84 in regression tests.
-Allow 'aa' or other values to be passed to label-units option.
-Make regression tests less sensitive to whitespace when comparing SVG files.
1.0.1 (Sep 11 2017)
-Add feat-type-regex to 'load-gene-expression-table'. Allows reading expression data
associated with RNA features rather than CDS features (the default.)
-Add 'circle' track type and regression test.
-Add new label functions: literal_text, product_name
-Add new color function: snp_type_incl_utr
-Modify LinearScale.pm to allow negative coordinates.
-Modify circleator.t to round circle (cx, cy) coordinates when comparing SVG.
-Undo bam_get_coverage.c regression from previous commit.
-Add util/add_snp_merged_table_columns.pl to convert between old and new SNP table formats.
-Remove incorrect radius attributes from rectangle elements used in SVG masks [Issue #33].
-Fix length_kb label function bug giving origin-spanning features negative lengths [Issue #32].
-Fix bug causing feat-track label references to create duplicate features [Issue #34].
-Fix bugs involving the packing of features that span the origin.
Some test results updated accordingly. [Issue #35.]
-Add file (in misc/convert_svg_to_png_with_chrome/) demonstrating PNG conversion with Chrome.
1.0.0 (Jan 13 2016)
-Add parser for clc_find_variations SNP/indel-finding tool.
-Add feat-tag-gt, feat-tag-gte, feat-tag-lt, feat-tag-lte. Previously only
lte (less than or equal to) and gte (greater than or equal to) were supported, via
feat-tag-min-value and feat-tag-max-value.
-Add overlapping-feat-track option.
-Add variant-base-histogram glyph
-Add configuration files and data for figures from 2014 Bioinformatics paper.
-Add utilities for extracting and log-scaling summarized coverage data from BAM files.
-Fix for possible integer overflow in samtools/bam_get_coverage: replaced int with long.
-Make regression tests less sensitive to platform and SVG module version [Issue #21].
-Make regression tests use the correct Perl executable [Issue #26].
-Tested on more recent Perl versions (5.18.2, 5.22.1) and Mac OS X 10.11.2 (El Capitan)
1.0.0rc4 (Oct 15 2013)
-Add --version option to report the current version/release number.
-Modify Build.PL so it doesn't install circleator.bak into /usr/local/bin/.
1.0.0rc3 (Oct 11 2013)
-Add missing MANIFEST file to avoid build error.
1.0.0rc2 (Oct 11 2013)
-Fix Build.PL to work with system-wide installs [Issue #12]
-Add --conf_dir option to circleator
-Modify circleator.t to save temporary/log dir if test(s) fail [Issue #2]
1.0.0rc1 (Oct 02 2013)
-Changed release numbering syntax to the more standard major.minor.revision
-Moved code to GitHub (https://github.com/jonathancrabtree/Circleator)
-Moved ExtJS GUI into separate GitHub repository ("Ringmaster")
-Added Build.PL
-Reinstated unknown sequence id warning when parsing flat file graph/heat map data.
-Fixed bug in get_track_features causing feat-track references to be incorrectly processed.
-Added font-width-frac option to allow overriding FONT_WIDTH_FRAC global on a per-track basis.
circleator-1.0alpha11 (Jun 04 2013)
-Bug fix: label-units=Gb was using the label "Bb" instead of "Gb"
-label-units is now case-insensitive i.e., label-units=mb and label-units=Mb will both work
-Added new tests for label-units
circleator-1.0alpha10 (Jun 03 2013)
-Added tests for: graph-type=line, graph-type=heat_map
-Bug fix for case where graph-type=heat_map and no colors or color palette are supplied
-Fixed typos in references to GCskew tracks in the predefined track documentation.
-Corrected track options (heat_map_*, target_bp) to use '-' instead of '_' (but code now allows either)
-Bug fix: ignore graph_baseline when graph-type=heat_map
-Bug fix: fixed discrete color assignment for graph-type=heat_map
-Added "Gb" as new option for label-units.
-Bug fix: user-feat-type option was being ignored.
-Added 'tag' label function for displaying arbitrary feature attributes/tags e.g., GFF attributes such as 'ID'.
circleator-1.0alpha9 (May 15 2013)
-Added 'heat_map' graph type plus support for Brewer color palettes from http://www.colorbrewer.org
circleator-1.0alpha8 (Apr 26 2013)
-Modified SNP_Table to allow IUPAC ambiguity codes.
circleator-1.0alpha7 (Apr 26 2013)
-Added compute-graph-regions glyph: identifies regions where graph value is above/below specified bounds.
-Added overlapping-feat-type filter: only features that overlap with a feature of the specified type will be selected.
-Modified admin/makePredefTrackDocs.pl to regenerate SVG and PNG images only for updated config files
-Updated predefined track documentation: added label-units, graph-type
-Improved scaled_segment_list warning when scale is set too high.
-Circleator now automatically reduces scaled-up regions to 75% of genome whenever they would otherwise take >= 100%
-Added parser for new gene cluster file format (Gene_Cluster_Table.pm), new load-gene-cluster-table glyph
-Added new options to support filtering genes by gene cluster signature:
gene-cluster-genomes, gene-cluster-signature, gene-cluster-analysis, gene-cluster-min-genomes, gene-cluster-max-genomes
-Added parser (SNP_Table.pm) for new SNP file format, "snp-table", compatible with CloVR-Comparative SNP output.
circleator-1.0alpha6 (Mar 20 2013)
-Bug fix for issue with parameters not getting passed to Circleator::SeqFunction classes.
-Added missing feature filters (clip-fmin, clip-fmax) to Circleator/Config/Standard.pm
-Bug fix for loading features onto reverse-complemented contigs: they are now reverse complemented too.
-Changed log message to not treat 'gap' and 'genome' features in --contig_list as contigs.
-Added line graph support to graph glyph.
-Added 'snp-no-hit-label' and 'snp-same-as-ref-label' options to snp_base.pm
-Updated snp_base and snp_base_no_indel SNP color functions to handle multiple alleles.
-Updated MergedTable SNP parser to explicitly record "No Hit" values.
-Updated MergedTable SNP parser to handle multiple alleles separated by "," or "/".
-Added computed 'num_no_hits' attribute to parsed SNPs.
circleator-1.0alpha5 (Feb 20 2013)
-primary_id is now set correctly in Circleator-created features (e.g., 'contig', 'genome'.)
-Added missing feature filters (feat-min-length, feat-max-length) to Circleator/Config/Standard.pm
-Fixed bug in Circleator/Util/Deserts.pm: compute-deserts glyph was throwing an error on linear sequences.
-Bug fix and changes to accomodate a new variant of the Skirret format.
-Added conf/clovr-microbe and 3 configuration files for the CloVR Microbe pipeline's output.
circleator-1.0alpha4 (Feb 15 2013)
-Minor documentation improvements.
-Added snp-intronic-color, snp-readthrough-color options to the snp_type color function.
-Added snp_type_no_indel color function, which is the same as snp_type but without the insertion and deletion colors.
-Changed the feature type of contig gaps (in multi-contig figures) from 'contig' to 'contig_gap'.
-Fixed off-by-one bug in the positioning of 'contig' and 'contig_gap' features in multi-contig figures.
-Added 'gff' feat-file-type, which uses the BioPerl GFF parser in Bio::FeatureIO::gff.
-Added contig-gaps predefined track.
-Added data/AE003852-AE003853.gbk, chrI and chrII of V. cholerae O1 biovar eltor str. N16961
-Fixed bug whereby additional feature filters on tracks using 'feat-track' were ignored.
-Added the following categories to the --debug command-line option: coordinates,input,loops,misc,packing
-Added optional 'revcomp' flag to --contig_list file format: including it on a line reverse complements the corresponding input contig.
-New tests for: multi-contig inputs, feat-file-type=gff, loops, nested loops, multi-contig inputs using --contig_list, reverse complementing input sequences
-Converted some warnings into debug messages to decrease default log verbosity.
-Fixed bug/clarified behavior in case where --contig_list file contains explicit gap features.
-A sequence id can be specified in --contig_list to override that found in the corresponding data file.