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CHANGELOG.md

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1.2.9 / 2019-10-13

  • Fix segfault triggered by length-zero sequences
  • Fix memory detection problem for some outdated MacOS versions
  • Fix an incorrect assertion in unitig graph refreshing
  • Added --verbose to output full log to the screen

1.2.8 / 2019-08-10

  • Add intermediate megahit_core_popcnt for CPUs that have ABM but not BMI2
  • Allow new assembly task with --continue

1.2.7 / 2019-07-28

  • Symbol link megahit_core_no_hw_accel to megahit_toolkit for backward compatibility
  • Better logging and for memory adjustment during SDBG building
  • Attempt to continue SDBG building even user-specified memory size is not sufficient

1.2.6 / 2019-07-13

  • Refactored and fixed a bug in local assembler
  • Refactored megahit script
  • Obtain total memory size from os.sysconf
  • Fixed segmentation fault in Mac OS with clang 4.0
  • Added --cleaning-rounds and --disconnect-ratio options for more flexible graph cleaning control

1.2.5-beta / 2019-06-28 PST

  • Fixed a bug that causes higher memory usage in seq2sdbg
  • Refactor on sequence sorters, edge I/O and contig I/O

1.2.4-beta / 2019-05-25 PST

  • Fixed a few memory leaks
  • Use std::vector to replace malloc in SDBG builders
  • Try to fix potential problem caused by benign data race in unitig graph refreshing
  • Faster by using phmap and xxh3

1.2.3-beta / 2019-05-12 PST

  • Refactored sequence readers
  • Fixed a bug in SDBG building of large k-mer sizes

1.2.2-beta / 2019-04-16 PST

  • Automatically detect POPCNT/BMI2 and select the correct megahit_core binary

1.2.1-beta / 2019-03-30 PST

  • Added --no-hw-accel option for users whose CPUs do not support BMI2/POPCNT
  • Added --test option for testing
  • Compilable with CMake 2.8 and g++4.8

1.2.0-beta / 2019-03-24 PST

Heavily refactored the whole project:

  • Remove GPU support
  • Use cmake
  • Use sparsepp to replace IDBA's hash map for better performance in both speed and memory efficiency
  • Use pdep instruction to speed up rand and select
  • Rewrite unitig graph
  • Rewrite the iterate-edge component
  • Rewrite the SDBG library, except for the builder
  • Fixed a bug which may involve too many reads into local assembly

The changes result in a faster and more memory-efficient tool, but have little effect on assembly quality.

1.1.4 / 2018-11-01 PST

  • Fixed a bug in mercy edge stage in 1-pass mode

1.1.3 / 2018-03-02 PST

  • Fix a bug in atomic bit vector that may cause a race condition

1.1.2 / 2017-08-01 HKT

  • Hotfix of an integer overflow bug

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