Automation, Refactoring, and Mismap Fixes #20
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added 18 commits
March 20, 2024 23:09
…column diff in renaming contigs. Replaced awk script with py script that chooses concensus ref chr to avoid multiple chr mappings to one contig.
…chm13 RM annotations.
…ules. Removed unnecessary conversion of unaligned bam to fq.
…lculation. Bump memory for nucfreq and fix hap pattern to account for hifiasm contig naming convention.
…e. Added rules to rename assemblies. Added intersecting of alignment bed with monomeric pqarm to reduce num of aligned contigs. Moved/renamed some config vars around so cleaner.
… Add back second alignment to cens only. Handle hifiasm format differences. Set minimap2 version to v2.26 fixing issues with piping to samtools view.
…dirs for dna_brnn to avoid cluttering.
…flow to avoid clutter and work with longer contig IDs. Fixed count_complete_cens rule to account for partial contigs.
…oring humas-hmmer to work with prev changes. Remove unused scripts. Allow setting input start and end columns for filter_cen_ctgs.py. Added map_cens.py.
…v row chm1 output to include contig coords. Added cen-stats and remove check cen status script. Allowed plot script rules to skip empty files. Removed sed splits which can fail due to contig id name differences. Refactored/categorized outputs into subdirs. Changed map_cens to use percent identity by events instead of all. Decreased legend size of repeatmasker plot. Adjusted stv_row output to include contig start coord. Updated StainedGlass submodule with updates to correctly include output dir. Removed inaccurate as-hor length output.
added 2 commits
April 7, 2024 22:15
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count_complete_censrule to count complete centromeres after accounting for partial centromeres.arr_len_thrparams incalculate_HOR_length.pyto prevent including small HOR arrays.calculate_HOR_lengths.py#14calculate_HOR_length.py.calculate_HOR_length.pywith incorrect length difference calculation.NucFreqmisassembly detection withNucFreqfork.minimap2v2.26 as v2.27 omits MD tag in SAM header causing failure in piping tosamtools view.awkcommands to avoid usingsed-split inputs which can fail with different ID formats.