Circleator v1.0.2

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.

Circleator v1.0.1

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.

Circleator v1.0.0

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)

Circleator v1.0.0rc4

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/.

Circleator v1.0.0rc3

1.0.0rc3 (Oct 11 2013)

• Add missing MANIFEST file to avoid build error

Circleator v1.0.0rc2

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]

Circleator v1.0.0rc1

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.