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factor out analyse_single_sequence function main #186: Commit 47fde59 pushed by Donaim
March 12, 2024 20:12 8m 12s master
master
March 12, 2024 20:12 8m 12s
aligned_sequence: tolerate index out of bounds main #185: Commit 43efacd pushed by Donaim
March 12, 2024 20:12 8m 15s master
master
March 12, 2024 20:12 8m 15s
catch codon error in main main #184: Commit 3f90930 pushed by Donaim
March 12, 2024 20:12 7m 45s master
master
March 12, 2024 20:12 7m 45s
add missing import main #183: Commit 7a7e5a0 pushed by Donaim
March 12, 2024 20:12 7m 51s master
master
March 12, 2024 20:12 7m 51s
move find_orf into its own source file main #182: Commit 94c3e48 pushed by Donaim
March 12, 2024 20:12 10m 31s master
master
March 12, 2024 20:12 10m 31s
move shared classes to their own source files main #181: Commit 3a216a2 pushed by Donaim
March 12, 2024 20:12 8m 48s master
master
March 12, 2024 20:12 8m 48s
void direct use of AlignedSequence.map_index main #180: Commit 59c576a pushed by Donaim
March 12, 2024 20:12 8m 30s master
master
March 12, 2024 20:12 8m 30s
avoid direct use of coordinates mapping in has_reading_frames main #179: Commit deb2d95 pushed by Donaim
March 12, 2024 20:12 9m 16s master
master
March 12, 2024 20:12 9m 16s
hide all mafft uses behind AlignedSequence main #178: Commit f950e4e pushed by Donaim
March 12, 2024 20:12 8m 15s master
master
March 12, 2024 20:12 8m 15s
make AlignedSequence abstraction main #177: Commit d30c6cb pushed by Donaim
March 12, 2024 20:12 8m 26s master
master
March 12, 2024 20:12 8m 26s
remove redundant type cast main #176: Commit aba8d2c pushed by Donaim
March 12, 2024 20:12 6m 57s master
master
March 12, 2024 20:12 6m 57s
use precise distance metric when searching for ORFs main #175: Commit 5fb3c0b pushed by Donaim
March 12, 2024 20:12 6m 58s master
master
March 12, 2024 20:12 6m 58s
factor out detailed_aligner main #174: Commit 6138ee8 pushed by Donaim
March 12, 2024 20:12 6m 58s master
master
March 12, 2024 20:12 6m 58s
normalize distance to [0, 1) with f(average_dist) = 0.5 main #173: Commit a4d5c39 pushed by Donaim
March 12, 2024 20:12 6m 50s master
master
March 12, 2024 20:12 6m 50s
add orfs_coverage data to holistic.csv main #172: Commit 7394784 pushed by Donaim
March 12, 2024 20:12 6m 57s master
master
March 12, 2024 20:12 6m 57s
include subtype positions to orfs.csv main #171: Commit d3678f7 pushed by Donaim
March 12, 2024 20:12 6m 21s master
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March 12, 2024 20:12 6m 21s
add qlen to holistic info main #170: Commit 355d219 pushed by Donaim
March 12, 2024 20:12 6m 44s master
master
March 12, 2024 20:12 6m 44s
fix calculation of blast_sseq_coverage main #169: Commit ca49f71 pushed by Donaim
March 12, 2024 20:12 6m 40s master
master
March 12, 2024 20:12 6m 40s
fix typo in holistic field name main #168: Commit 9a36671 pushed by Donaim
March 12, 2024 20:12 6m 36s master
master
March 12, 2024 20:12 6m 36s
Add another output file: holistic.csv main #167: Commit 022ee3d pushed by Donaim
March 12, 2024 20:12 9m 9s master
master
March 12, 2024 20:12 9m 9s
Catch invalid codon errors main #166: Commit 76f0401 pushed by Donaim
March 12, 2024 20:12 6m 31s master
master
March 12, 2024 20:12 6m 31s
regenerate blast database main #165: Commit fe682b4 pushed by Donaim
March 12, 2024 20:12 6m 36s master
master
March 12, 2024 20:12 6m 36s
catch alignment error main #164: Commit 473313e pushed by Donaim
March 12, 2024 20:12 9m 1s master
master
March 12, 2024 20:12 9m 1s
do not assume that expected orf is nonempty main #163: Commit 4c11e3a pushed by Donaim
March 12, 2024 20:12 9m 3s master
master
March 12, 2024 20:12 9m 3s
remove dashes from subtype alignments main #162: Commit c49975d pushed by Donaim
March 12, 2024 20:11 7m 7s master
master
March 12, 2024 20:11 7m 7s
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