Version 0.7.2 alpha 1

• feat[viz]: toggle-able Gaussian curves
• fix[call]: properly skip reads with no name
• fix[call]: .item() call error when not in targeted mode
• chore[call]: remove deprecated cigar tuple access
• chore[call]: remove a duplicate variable assignment
• chore[call]: add more type hinting
• chore: update dependencies

Version 0.7.1

• fix: running without args giving error instead of help

Version 0.7.0

• feat![call]: don't indent JSON by default for a more compact representation
  • can be re-enabled with the --indent-json flag
• feat![call] more compact read data representation in JSON reports
• feat[mi]!: add bin totals / loci total for JSON MI reports
• chore!: remove old broken aligned-lengths command
• chore: set default log level to info
• feat[call]: output genotyping progress for large catalogs
• feat[call]: warn if a call takes an excessive amount of time
• feat[call]: report adjusted reference coordinates separate from original catalog coordinates in JSON report
  • this fixes Mendelian inheritance/error reporting from the strkit mi function
• feat[mi]: add --exclude-loci-bed file to exclude specific loci from MI calculations.
• perf[call]: large optimization to reduce time needed to find flank coordinates
  • uses modified binary search (O(log n)) rather than searching through read (O(n)) where n is the length of a given read
• perf[call]: minor optimizations
• perf[call]: switch to using k-means++ for GMM initialization
• perf[call]: fix performance regression from realignment feature
• perf[call]: don't try to sort results if single processed
• perf[call]: minor performance tweaks with looping/timing of object&variable initialization
• perf[call]: early return if we definitely don't have enough reads to start calling
• feat[call]: improve locus call time in JSON report
• fix[call]: caching not working for GMMs - performance should be improved now
• feat[call]: --hq flag to turn on/off expansion exception for 'smoothing' genotype filter
• refact[call]: move allele.py GMM generation code into its own function
• fix[call]: fix strange logging behaviour with process-specific loggers
• chore[call]: increase logging progress interval to 120 seconds
• docs: emphasize importance of hq and realign flags
• fix[mi]: spurious warning about multiple testing
• fix[mi]: GangSTR not using correct coordinates for checking TRF catalog
• feat[call]: include read strand in JSON report
• feat[viz]: show k-mer bar plot in overview
• feat[viz]: show report parameters/metadata in new tab
• chore[viz]: update igv.js
• style[viz]: use palette colours for distributions and tweak colour ranges
• docs: add flowchart and update browser screenshots
• chore: bump dev dependencies

Version 0.7.0 alpha 15

• fix[mi]: Straglr again
• style[viz]: use colour scales for calls and 95% CIs

Version 0.7.0 alpha 14

• fix[mi]: make locus totals more intuitive and fix totals for Straglr
• fix[mi]: missing locus counting in some calculator classes
• chore[mi]: make MIContigResult always truthy

Version 0.7.0 alpha 13

• feat[mi]!: add bin totals / loci total for JSON MI reports
• refact[call]: move allele.py GMM generation code into its own function
• fix[call]: fix strange logging behaviour with process-specific loggers
• chore[call]: increase logging progress interval to 120 seconds
• docs: emphasize importance of hq and realign flags

Version 0.7.0 alpha 12

• perf[call]: large optimization to reduce time needed to find flank coordinates
  • uses modified binary search (O(log n)) rather than searching through read (O(n)) where n is the length of a given read
• perf[call]: minor optimizations
• chore[call]: make progress worker nicer
• chore[call]: nicer logging for over-long calls
• fix[call]: double logging in single-processing mode

Version 0.7.0 alpha 11

• fix[call]: progress display code crashing in multi-processing mode
• fix[call]: logging not working in multi-processing mode

Version 0.7.0 alpha 10

• feat[call]: warn if a call takes an excessive amount of time

Version 0.7.0 alpha 9

• feat[call]: output genotyping progress for large catalogs
• chore: set default log level to info