Timofey Prodanov

Mappy fails while calling cigar_str if you use X/= instead M

4

If you align sequences using `mappy` and using `0x4000000` flag (use X and = instead of M in CIGAR), and then if you try to print hits or print `cigar_str`,...

[Here](https://dl.dropboxusercontent.com/s/kjpfibgvyaanebz/test.tar.gz?dl=0) you can find two sequences. If you align them directly using `minimap2` ```bash minimap2 -ax asm20 1.fa 2.fa --MD -o test.sam ``` it works without problems. If you run...

Deletion at the end of the alignment

1

Secondary alignment has a deletion at the end of its cigar. Ways to reproduce (using human genome version 19): ```bash samtools faidx hg19.fa 7:157673851-157674750 > 1.fa bwa mem -a -k...

Update [Parascopy](https://github.com/tprodanov/parascopy) to version 1.9.0.

Imperfect read alignment, changing parameters does not help

9

Mapping a read ``` >A00297:159:HV2LVDSXX:3:1439:25572:32503 AGGCGGCCCCTGCAGTGGTCGCTGATGCAGGCGTTGAAGAATGGGCCCGGGGGCACAAGGTTGTGGCACTCAGCAAAGACCCTGTGGGGCAAAGCGATCAGGACGGAGGGCCCCCAGCGTGCATGCGGGCGGGCGGGGGCGCCCCAGGGC ``` to the reference ``` >ref CCCATGCCCACCACAGCCGCTCTGTGATCTGATGCTGAGCCAGTGAGTCCTCCCCTCGGG GGTTGCAGGCCCTGGGGCGCCCCCGCCCGCCCGCATGCACGCTGGGGGCCCTCCGTCCTG ATCGCTTTGCCCCACAGGGTCTTTGCTGAGTGCCACAACCTTGTGCCCCCGGGCCCATTC TTCAACGCCTGCATCAGCGACCACTGCAGGGCCGCCTTGAGGTGCCCTGCCAGAGCCTGA GGCTTACGCAGAGCTCTGCCGCGCCCGGGGAGTGTGCAGTGACTGGCGAGGTGCAACCGG TGGCCTGTGCGGTGAGTGGGGGCGGCCCCGGGCCCCCCAGACCCCTCGGCCTCTCTGAGT GTCCTGTGCGGTGAGTGGGGGCGGCCCCGGGCCCCCCAGAC ``` using Strobealign `v0.11.0` produces alignment `143=7S` with score 296. Mapping...

Backspace does not work in keybindings

6

Setting `set edit:insert:binding["Alt+Backspace"] = { echo A }` does not give any errors, but also will not do anything if I press `Alt+Backspace`. `xev` produces the following output: ``` KeyPress...

Slightly updated recipe for [Parascopy](https://github.com/tprodanov/parascopy) for v1.15.1

All secondary alignments lost

7

In the following data: [data.tar.gz](https://github.com/user-attachments/files/16457383/data.tar.gz) there is exactly one single-end short read in `input.fasta` and two sets of haplotypes, `full.fa.gz` and `subset.fa.gz`. Running Strobealign `v0.13` with the subset of haplotypes:...

Genome to protein does not work

1

I have R `4.5.1`, `emsembldb v2.32.0` and `EnsDb.Hsapiens.v86 v2.99.0`. Currently, the code from [this tutorial](https://bioconductor.org/packages/devel/bioc/vignettes/ensembldb/inst/doc/coordinate-mapping.html#2_Mapping_genomic_coordinates_to_transcript-relative_coordinates) does not work for me: ```r library(ensembldb) library(EnsDb.Hsapiens.v86) edbx

dxCompiler fails to compile example scripts like bam_chrom_counter

2

Similar to problems, [reported by this user](https://community.ukbiobank.ac.uk/hc/en-gb/community/posts/19662007504029-error-compiling-bam-chrom-counter-wdl?input_string=dxCompiler%20does%20not%20compiler%20example%20scripts), I cannot compile any WDL scripts on my machine, even standard ones like [HLA arcas](https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/tips-and-tricks/guide-to-analyzing-large-sample-sets) or [Bam chrom coutner](https://documentation.dnanexus.com/developer/building-and-executing-portable-containers-for-bioinformatics-software/dxcompiler). I have java ```...