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Recent Releases of viralconsensus

viralconsensus - ViralConsensus v1.0.0

  • Added support for the BAM_CREF_SKIP CIGAR string operation
    • Thanks, @rebeelouise!
  • ViralConsensus seems to be stable, so updating version to 1.0.0

- C++
Published by niemasd 10 months ago

viralconsensus - ViralConsensus v0.0.6

  • Added (hopefully) correct support for primers on the reverse strand (lines where column 2 > column 3 in the BED file)
    • Thanks, @RanWei1987!

- C++
Published by niemasd over 1 year ago

viralconsensus - ViralConsensus v0.0.5

  • Updated "Is this larger than the minimum frequency?" comparisons for stability
    • I used to do if(count / tot_depth > min_freq)
    • I changed it to if(count > tot_depth * min_freq)
    • count and tot_depth used to be double due to the division, but I changed them to unsigned integers
  • Changed all double to long double just in case floating point precision is an issue in edge cases
    • This is only relevant to comparisons against the minimum frequency to call bases/insertions
  • Changed most int/long integer types to int??_t and uint??_t types
    • This probably won't impact anything, but figured I would do it just in case for cross-platform stability

- C++
Published by niemasd about 2 years ago

viralconsensus - ViralConsensus v0.0.4

  • Open the reference genome of an input CRAM file properly
    • Originally, CRAM files were always pulling a remote copy of the reference genome (https://github.com/niemasd/ViralConsensus/issues/6)
    • To fix it, I used the htslib cram_load_reference() function, which solved the immediate problem (https://github.com/niemasd/ViralConsensus/commit/0b99fcade0d3a6769a27819ee92bf77d6ebd2893)
    • However, it seems like this is an internal htslib function, and the proper fix is to use the hts_set_opt() function instead
    • Thanks for the fix, @daviesrob! And thanks for your input, @jmarshall and @jkbonfield!
    • This shouldn't change anything from the user's perspective: it just makes it easier to compile ViralConsensus

- C++
Published by niemasd over 2 years ago

viralconsensus - ViralConsensus v0.0.4

  • Open the reference genome of an input CRAM file properly
    • Originally, CRAM files were always pulling a remote copy of the reference genome (https://github.com/niemasd/ViralConsensus/issues/6)
    • To fix it, I used the htslib cram_load_reference() function, which solved the immediate problem (https://github.com/niemasd/ViralConsensus/commit/0b99fcade0d3a6769a27819ee92bf77d6ebd2893)
    • However, it seems like this is an internal htslib function, and the proper fix is to use the hts_set_opt() function instead
    • Thanks for the fix, @daviesrob! And thanks for your input, @jmarshall and @jkbonfield!
    • This shouldn't change anything from the user's perspective: it just makes it easier to compile ViralConsensus

- C++
Published by niemasd over 2 years ago

viralconsensus - ViralConsensus v0.0.3

  • Fixed bug where local reference genome file is ignored when using CRAM file
    • Prior to v0.0.3, when the input file is a CRAM file, htslib tries to automatically download the reference genome based on the MD5 hash: it ignores the user-provided reference genome FASTA file
    • As a result, ViralConsensus would sometimes crash in specific contexts when the running environment was unable to connect to the internet
    • Now, this issue should be fixed: it should be using the local file and should be working in offline contexts

- C++
Published by niemasd over 2 years ago

viralconsensus - ViralConsensus v0.0.2

  • Fixed bug when handling minority insertions with sufficiently high coverage (thanks @alexcritschristoph!)
    • Normally, if an erroneous insertion is encountered, the number of reads supporting that insertion should be low
    • However, if sequencing is deep enough, the number of reads supporting that insertion could exceed the "minimum coverage" threshold, even though there could be a ton of reads that don't have that insertion
    • E.g. if there are 100 reads with ACGT and 1,000,000 reads with ACT (no G), the ACGT would still appear in the consensus
    • To patch this, we now correctly count "no insertion" between matches/mismatches

- C++
Published by niemasd over 2 years ago

viralconsensus - ViralConsensus v0.0.1

  • Initial release

- C++
Published by niemasd about 3 years ago