 Jennifer Shelton | 2f86b94c4c9 | feat: removed old TC script | | |
Jennifer Shelton | 9cf9df2cdde | feat: script to describe read support in terms of read length | | |
Jennifer Shelton | 2e16ba208a9 | feat: mark duplicates if TF occurs in both reads | | |
Jennifer Shelton | 4428b92869c | feat: record teloRead sequence next to characteristics | | |
Jennifer Shelton | da9535999fe | draft: tf | | |
Jennifer Shelton | bbe05dff6bb | feat: run EdgeToInternalRatio without attempt to estimate TL | | |
Jennifer Shelton | 3262082114c | feat: make executable | | |
Jennifer Shelton | 5aae5fd630f | fix: restart automatic duplicate countingprint empty table if coverage is too low for a length estimate | | |
Jennifer Shelton | 35423dfd955 | feat: only count dup reads in gc-match regions | | |
Jennifer Shelton | f27309cc3c6 | fix: typo | | |
Jennifer Shelton | dffe5de5df8 | fix: typo | | |
Jennifer Shelton | 17934ad930d | fix: typo | | |
Jennifer Shelton | ee6fbc2a2f6 | feat: typo | | |
Jennifer Shelton | 992567d367b | feat: run single end reads | | |
Jennifer Shelton | a86db6520de | fix | | |
Jennifer Shelton | bc70d68de58 | fix: count dups | | |
Jennifer Shelton | b6ad6d02dc4 | fix: trimmer reads fastq | | |
Jennifer Shelton | ecb4fc71a4f | fix: trims | | |
Jennifer Shelton | 1ca23e5d5a0 | feat: add untrimmed ratio | | |
Jennifer Shelton | 977d5a407aa | feat: add noncanonical kmers | | |
Jennifer Shelton | d81cf18350d | fix: minor changes | | |
Jennifer Shelton | 39536f24572 | fix: typo | | |
Jennifer Shelton | 1b10d820594 | fix: typo | | |
Jennifer Shelton | 3fff1f474a7 | feat: prep for T2T alignment | | |
Jennifer Shelton | 9fa9573e84b | feat: pass SAM line | | |
Jennifer Shelton | 951ae7e2112 | docs: update docs | | |
Jennifer Shelton | 50cff7bcfd0 | docs: update diagram | | |
Jennifer Shelton | ed323aa9bed | fix: typo | | |
Jennifer Shelton | 650e36e8d37 | fix: handle parent dir at root | | |
Jennifer Shelton | 92c195638f7 | feat: filter for canooical and non-canonical telomeric repeats in read | | |
Jennifer Shelton | 70a4b2e7ab6 | fix: minor path issue | | |
Jennifer Shelton | 03683f32bbdM | pull online changesMerge branch 'main' of https://bitbucket.nygenome.org/scm/compbio/telomeasure | | |
Jennifer Shelton | 96c1ed863ec | fix: python3 adjustments | | |
Jennifer Shelton | 7821bd0ba13 | feat: gracefully fail when no reads align to the pseudo telomere or are sent for alignment after initial filtering | | |
Jennifer Shelton | dde5c799768 | docs: round coverage on plot | | |
Jennifer Shelton | 3fa6d19f99d | fix: python3 adjustments | | |
Jennifer Shelton | 1361a081f08 | feat: gracefully fail when no reads align to the pseudo telomere or are sent for alignment after initial filtering | | |
Jennifer Shelton | 07beb9629e4 | init: telomeasure scripts | | |
