v0.2.1

Changelog

New features

• Introduce a new analytical module titled 'Errors in Read Position,' which encompasses two subcategories: @Ming-Lian

  • Errors in Short/Long Reads, featuring a visual representation of the occurrence and frequency of error events in a random sample of 200 reads. The section for short reads (not exceeding 6kb in length) is ordered by descending length, while the long reads section (exceeding 6kb) is selectively presented with 2kb from the start, middle, and end, and sorted by the frequency of error events in the initial 2kb segment in descending order.
  • Errors in Read Position, visualizing the frequency and error rate of error events at each base position within 10kb from the 5' end of the read, with attention to the fact that the actual results displayed in the figure have been smoothed over windows of 50bp. The outcomes of this module are archived in the web report under 'Reference-based QC / Sequence Accuracy / Errors in Read Position'.

  

  

  

• A newly introduced analytical module, "Errors near Homo/Heteropolymer," which consists of two subcomponents: @Ming-Lian

  • Proportion of Errors near Homo/Heteropolymer, statistically evaluates the proportion of error events such as Deletions, Insertions, and Mismatches occurring in the vicinity of homo/heteropolymer regions, which serves to estimate the contribution of homo/heteropolymers to the occurrence of various error types.
  • Proportion of Errors near Homopolymer with Respect to Homopolymer Length, quantify the distribution of errors, specifically Deletions, Insertions, and Mismatches, near homopolymer regions of varying lengths. The analytical outcomes of this module are archived within the web report under the section "Reference-based QC / Low Complexity Regions / Errors near Homo/Heteropolymer".

  

• Save some statistics results into intermediate files through pickle; @Ming-Lian

Bugfixes

• Incorrect logic for calculating BAM global statistics "Total_reads"; @Ming-Lian
• Fail to remove chromosomes without enough length when plot genomic coverage; @Ming-Lian
• Incorrect caculation for query position in supplementary alignments; @Ming-Lian

Enhancements

• Adaptive chunk_size setting based on chromosome length and number of threads to make parallel effective; @Ming-Lian