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.

v1.1.3

• Reduce peak memory.
• Add more error report.
• Fix some error without exit.

v1.1.2

1.1.2

• Fix a bug that AssemblyMapper cannot overwrite existing telomere checking result.
• Fix a bug that small number of N repesenting unknown bases are identified as gap.

v1.1.1

• Fix a bug that CentroMiner stuck after v1.0.4