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ChangeLog.md

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1.1.1 / 2016-12-08 HKT

  • Added -f option to force overwrite output directory
  • Added --bubble-level option to control bubble merging; though level 3 (i.e. super bubble) is not mature (default level is 2)
  • Optimized the speed of tips removal

1.1-beta / 2016-11-30 HKT

  • Added components to better handle high depth errors
  • Added components to merge super bubbles
  • Fine tuning k-mer sizes to support longer reads (150bp)
  • In general, it produces longer contigs compared to previous versions

1.0.6 / 2016-06-06 HKT

  • Fixed a bug that ignores edge multiplicity at all. This bug existed since v1.0.4-beta

1.0.5 / 2016-05-17 HKT

  • Removed the requirement for CPU_thread >= 2.
  • Added the --tmp-dir option
  • More user-friendly error message when seeing bad pair-end files
  • Fixed a bug that may stop an assembly earlier

1.0.4-beta / 2016-02-16 HKT

  • Faster index of succinct de Bruijn graph via prefix look up
  • Add --prune-level 3 and --prune-depth options for more aggressive pruning
  • Tune bulk parameters
  • Support reads with length >= 65536 bp

1.0.3 / 2015-10-11 HKT

  • Hotfix of number of tip nodes in SdBG 32 bit integer overflow

1.0.2 / 2015-08-15 HKT

  • Fixed a bug when number of large multiplicities > INT_MAX
  • Fixed dead loop in local assembler when # of reads is 0
  • Use mmap for edge/sdbg IO
  • Correct the rounding of edge multiplicity from float to integer

1.0.1 / 2015-07-31 HKT

  • Fixed number of SdBG edges 32-bit integer overflow.

1.0.0-beta / 2015-07-23 HKT

  • --presets option: preset parameters for different types of assembly
  • New CPU sorting design: faster kmer counting & graph construction
  • New unitig graph and edge multiplicity design: more accurate assembly
  • Merge bubble carefully at small k: reduce the occurrences of bubble collapsing

0.3.3-a / 2015-07-04 HKT

  • Hotfix of incorrect max read length of multiple library
  • Hotfix of --input-cmd idling

0.3.3 / 2015-07-04 HKT

  • Fixed segmentation fault when a read is all N
  • Fixed continue mode: check continue mode before writing binary reads
  • Slightly improve SdBG traversal functions

0.3.2-beta / 2015-06-28 HKT

  • fine tune local assembly multi-thread schedules
  • fine tune SdBG builder memory usage

0.3.0-beta3 / 2015-06-22 HKT

  • --verbose option
  • fixed a bug when reading paired-end reads of different length
  • print assembly stats to the end of the screen message
  • print read libraries info to the screen message, and number of reads in each libraries to the log file

0.3.0-beta2 / 2015-06-20 HKT

  • added the missing file citycrc.h

0.3.0-beta / 2015-06-18 HKT

New features:

  • --max-read-len parameter no longer required
  • --memory option set to 0.9 by default
  • make use of PE informations (with local assembly)
  • --prune-level and --merge-level for setting pruning and merging intensity
  • --kmin-1pass option for assembling ultra low-coverage datasets in less memory
  • supporting bzip2 input files
  • useful tools in megahit_toolkit, including contig2fastg for conversion of contig files into SPAdes-like fastg

0.2.1 / 2015-03-18

Bug Fixes:

  • Fixed incorrect mercy kmers searching when read length >= 255
  • Minor bugs (huge log in some edge cases, etc.)

New features:

  • Semi-auto memory setting: when 0 < "-m" < 1, use fraction of the machine's memory
  • --out-prefix option
  • --cpu-only turn on by default, and --use-gpu option to enable GPU
  • python3 compatibility

0.2.0 / 2015-01-30

Bug Fixes:

  • Fixed "option --num-cpu-threads not recognized"

Enhancements:

  • --mem-flag option for memory control
  • --continue option to resume an interrupted run
  • support mixed fasta/fastq input via kseq.h

0.1.4 / 2015-01-20

Bug Fixes:

  • Fixed crashes related to OpenMP

0.1.3 / 2014-12-01

Enhancements:

  • MAC OS X support
  • Minor improvement to reduce memory usage of the SdBG builder

Bug Fixes:

  • Fixed crashes in some edge cases

0.1.2 / 2014-10-10

Enhancements:

  • Update Makefile and python wrapper to improve compatibility
  • Output exit code when subprogram exit abnormally
  • Improve memory usage of the subprogram assembler
  • Fix the issue of minor stat differences caused by loops

Bug Fixes:

  • Use get_ref_with_lock() to ensure hash_map being thread-safe when updating values
  • Correct the computation of edge multiplicity when iterate from small k to large k
  • Fix a bug that cause segfault in the subprogram sdbg_builder

0.1.1 beta / 2014-10-02

Enhancements:

  • Add change log
  • More detailed README for input format
  • Use CompactSequence in UnitigGraph
  • Remove unused parallel sorting codes

Bug Fixes:

  • Fixed wrong computation of word_per_read in cx1_functions.cpp
  • Fixed crash in FastxReader if the file is empty
  • Fixed floating point error in assembly_algorithms.cpp