Jamie McGowan

Probably due to markdown extensions not loading correctly.

Is it possible to keep coverage/count information when using `merge_linear_paths`? E.g., this is snippet of my starting graph which has FC tags: ``` S 35 TATTTTTATTAGAGACCTTGATTCCGATAATATTCATGTTGTATTAGCCGATTTTGGTCTAGCCAAAGCAAGTATGGGTTCAGTTGACAGATCCTATGCTGGCACTCCTTTATACATGTCTTTAGAACTCGCAACCGGAGGAAAGTACAGTTTCAATACCGATATCTATTCATTGGGAGTGGCTATCTATCAAATCATGACCAAAGACACAACCACAGCTGTCAGTCACATGTTTATTTCGAATAGAGAGGAAGAAGCAATTGATAAATTAACAAAGGAAATGGAAAAATCAGGAAATTATTCAACAACATTGATTAATATTTGTTTATCTATGCTGGAGAAGGATGCCAGTAAGAGACCAAGTGCCAAGCAAATCCTTTCCAATACTTTCTTGGAAGATATTCTCATCACACCAACAGAATAAACAATTTCTTGTGTTTTACCGCTGAAGTTAACCGTTAGAATTATAATAATTTTATTTTTCACAACAAAAAAAACAAGCCAACAACAATAGAGCGGGTGCAAACTCGGGTGTATCTACCGTTTTTCGTTTCTGAAAACGACTTTCGTTTTTGTTCGTGTTTGAATGAAGATTTTTGGTGTTTCTTTCAAATTCATACAAGATCGTTTTTCGTTTTTGTAAAAAGTTAGAAAAATACGAAAACGTGGCAAGTTGCACCTGCTCTAATGTGGGCAACAAACTTGAGGTTACCATTACCTTCTTGAATGATCATCAGAAGATTATTCATCTTCGCTTACCATCAGAGATCTGATTATTAACCGCTCTTGACTGTCAACTGAGATTTGGCAGGTGAAATTCAGTTTTCACATTCGCCAAAAGAAAATGAAGATAAATGATGATGAATTGAATAATTCTTGAATTTCTTCCTACGGATAGCTATGCATCATTCTCACATATCAATAGGCAGTGTCAATCTATTCTTGTTTCGGAAAAACCAAACTTTTGGAAACAGAAAAAGAGTGAATATGATAGAACTATTGCCAACCAAGAACGATACCTCGACCATGTTATTGATACAATGACAAGAAATGCTTCTAAGAACAATTATTGTTTATTTGCTTGTTTTGTCGGGATGTTGTTTTCGTTTCTTGTGTTTTTACCAGCATTTATGATCATGGTGATTATGGCATCTAGTTCCCTTTCAGGAAATATATTGAATTGTGAGAGGAATGTTTCTTCTATTCAAGTTTTGAATAGAACTATTGAAAGGGTTTCTTATCCAGGATGTGTAGAATGTAACACAATTTGGAATACTAGTTGCAATAATTTCAATGTTATGCCATGTTGTCAACCAAATAATAGTTATTCTTCAATTTTCTCATATGAATGCAATGTAACTGAATGCATTAAGGAAAATTATCAAGATGGACCTCTCAGATGTCGAGTAATTAGTTACAACAACAAAAAAGGGCCATCCACATATTCACTAGTCATTTACAAACCAGAAAGCAATTATTCAGGGTCTATAGGACTATTATCTGGTTAGCTACCAATACTTATGATTTGAAAGTTTAGTCAGATTACTGAAATACTGACTTTATTTCACTAACAACACGTAGGTCGGCAATGTGATTCCTTCTTCATAATTGAGTATTAATCGTACGGTATTTGCAAGTAAATAATAACTAATAATGGTCAATTAACAAAATATTAAATAAATTATTTAAAAAAAATGAAAAGAAGCAGAGAGGAGGAACCTGCTGTTACCAATACATCATGTACTGATCAAAGTAATACAAGTTCCGATCCTCTCTTGGAAACGAATCTAAAAAAACAAGTGACTGGCAATATTT ll:f:44.5 FC:i:80768 kl:f:44.5 S...

"*run_*" in directory name

1

Having "`*run_*`" in the BUSCO output directory name causes an error (e.g. BUSCO5_rerun_XYZ_output) https://github.com/jamiemcg/BUSCO_phylogenomics/blob/0589f6ce883c3ebfa3b7521339d8caaf7f8bc526/count_buscos.py#L44-L49 (It looks for BUSCO sequences in the "logs" directory as it thinks it is the run...

Sometimes, recovered BUSCOs are flagged as being "fragmented" even though they are full length (due to divergence from ref db). Add an optional flag "--include-fragmented" for these sequences to be...

Add this: ``` print("\t".join(["\t"] + [busco_sample_name for busco_sample_name in busco_sample_names])) ``` Here: https://github.com/jamiemcg/BUSCO_phylogenomics/blob/0589f6ce883c3ebfa3b7521339d8caaf7f8bc526/count_buscos.py#L134-L145

Poor performance on very large files

4

Currently the live preview, status bar, word count are updated after every key stroke. Better to add delay or limit. This is related to #5

Even when enclosed in speech marks