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ChangeLog
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ChangeLog
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V 0.1.1
- Original release
V 0.1.2
- Added the updateOases script
- Coded in default parameters
- Amended Makefile
- Small error in gap distances
- Added test dataset
- Now outputs unused reads
- Counts reads used in assembly
- Minimum transcript length can be imposed
- Merged plausible and highly expressed transcripts
V 0.1.3
- Modified Makefile to eliminate side effect on Velvet installation
- Minimum gap length in fasta file is set at 10 bp
- Corrected crashing bug when printing UnusedReads file
- Eliminated empty transcripts
V 0.1.4
- Removed erroneous lines in Makefile
- Corrected mistake in length of gap
V 0.1.5
- Unused reads now selected properly
- AFG output available
- Colorspace now handled explicitly
V 0.1.6
- Compilation warning avoided
- Changed numbering of loci and transcripts in output to 1-based indexing
- Bug in setting min_pair_count
- Added the paired_cutoff parameter
V 0.1.7
- Correction to manual
- Corrected bug which added lots of gaps
- Added -scaffolding option
V 0.1.8
- Updated manual
- Reduced number of N gaps
V 0.1.9
- Further reduced number of artificial 1bp gaps
- Crashing bugs when running in the absence of short reads
V 0.1.10
- Compilation warnings addressed
- Missing long read connections corrected
- Missong short read connections corrected
V 0.1.11
- Compatibility issues with Velvet 1.0
- Output of alignments
V 0.1.12
- Compatibility with Velvet 1.0.06
- Removal of near-identical transcripts
V 0.1.13
- Inversion of bubble smoothing and coverage cutoff
- Weakened the '-scaffold no'
- TourBus loss of connections bug
V 0.1.14
- Strand-specific read orientation.
V 0.1.15
- Increased paired-end sensitivity
- Weakened the 'scaffold no' clipping
V 0.1.16
- Compilation warning
- Compatibility with latest Velvet
V 0.1.17
- Confidence score bug for singleton contigs
- Transcript count bug for loci with short transcripts
V 0.1.18
- Updated readme file
- Reverted default minimum transcript length to 100bp
V 0.1.19
- Corrected the output of contig sequences to match the length cutoff
- Conservative coverage cutoff for long sequences (mergeing)
- Penalty for hairpin assemblies
V 0.1.20
- Compatibility with Velvet 1.1.x
- Repeated transcripts - some left due to initial short nodes
V 0.1.21
- Compatibility with Velvet 1.1.03+
V 0.1.22
- POSIX compliant Makefile
- Velvet compatible Makefile
V 0.1.23
- Variable sizes for sequence lengths
- Heuristics to remove totally spurious connections
- Explicit merge function
- Some code cleanup
V 0.2.01
- Merge option
- Pipeline script
V 0.2.02
- Bundled zlib pointer in Makefile
- Ubuntu linking problem in Makefile
V 0.2.03
- Compatibility with Velvet 1.2.x
V 0.2.04
- Updated Manual
- Pipeline script fixed to work with inclusive intervals
- Improved redundancy filters
V 0.2.05
- Updated pipeline script for subprocess change
- Increased default MAXKMERLENGTH
- Bug in sorting nodes in filterTranscripts
V 0.2.06
- Bug in Python
- Streamlined merging
- Updated manual
V 0.2.07
- Massive refactoring of the code
- Bug with confidence > 1
- Reduced the amount of unwanted gaps in assemblies
- Memory corruptions
- More consistent removal of transcripts when merging
V 0.2.08
- Reads binary sequences files
V 0.2.09
- Store stats in Log file
- Use github submodule for Velvet dependencies
- Migrate documentation to Markdown
- Add --version option
- Add --citation option