v1.2.4

• Add new '--teclade' and '--teminrepeattimes' option for AssemblyMapper to control the behavior of built-in TeloExplorer.
• Add new '-a' option for GapFiller to select unimap as aligner. (Also fix the bug that default aligner not set in GapFiller after v1.2.3, thanks to a927050047, PR #46)

v1.2.3

• Add new '--extract-ref-flanks' option for AssemblyMapper, which allow chimeric contig output for gap filling. (see issue #42 for detail)
• Support Unimap as aligner. As a optimized version of minimap2, it still use the '--minimapoption'.
• Fix a bug that monopolizer contig length standard is too high.
• Deprecate the web server for maintenance issue (sorry!).

v1.2.2

• Add new '--keep' option for AssemblyMapper, which add all unplaced contigs in the draft genome.
• Add a new output AGP file for GapFiller to describe the modified chromosome structure.
• Fix another bug that cause small number of N representing unknown bases are identified as gap.

v1.2.1

• Fix a bug in CentroMiner that ploting halted when optional gene/TE annotation file is not given.

v1.2.0

• CentroMiner is refactored. It can receive gene annotation as well now. The output has only 2 folders now: TandemRepeat (fasta, gff3 of TR) and Candidate (candidate info and TR, TE, and gene content line chart, require ggplot2). TE data is removed from candidate info. It is recommended to check the line chart to decide which candidate you vote.
• '--noplot' option is added to each module. With this option, any ploting will be skiped. If you have problem in graphical issue, try this option.
• CloserScore in GapFiller detail is changed to CloserIdentity.
• Due to the major changes, the web server version of quarTeT will not be updated to the newest version for now.

v1.1.8

• Gapfiller will throw a warning instead of error when flanking sequence contains gap.

v1.1.7

1.1.7

• Support RepeatMasker's TE annotation format for CentroMiner module.

v1.1.6

1.1.6

• add new option 'maximum TR length' (-r) for CentroMiner to avoid trf stuck. (Thanks to atotickov, PR#22)
• disable unstable 'join' mode for GapFiller by default. Use '--enablejoin' option to enable this mode. '--fillonly' option is removed.

v1.1.5

• SVG output is moved to work dir instead of tmp dir. Intermediate file for figure drawing is saved to tmp dir instead of auto-remove.
• Fix a bug that running multiple quarTeT in one folder may cause error due to intermediate file overwrite.
• Fix a bug in AssemblyMapper that with option '--nofilter', contigs shorter than 50000 bp are still marked as too short and count in discarded length.
• Fix a bug that error in R figure drawing is not reported.

1.1.4

• Fix a bug in AssemblyMapper that large dict tmp file not write properly.
• Reduce more peak memory.
• Add a memory insufficient error report.