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quota-alignment

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Analyzed 12 months ago. based on code collected 12 months ago.

Commit Message	Contributor	Files Modified	Lines Added	Lines Removed	Code Location	Date
Jan 17, 2023 — Jan 17, 2024 Showing page 3 of 7 Search / Filter on:
add brentp's adjust_evalue as a blast filter, remove top_N filter	tanghaibao as Haibao Tang	More...				almost 15 years ago
readme	tanghaibao as Haibao Tang	More...				almost 15 years ago
+ add --format option to quota_align.py so it can take a .raw file directly, without having to convert via cluster_utils. + move all logic for file types. into read_clusters.	brentp	More...				almost 15 years ago
skip self-self hits (even if tandem_Nmax is not specified).	brentp	More...				almost 15 years ago
fix typo	tanghaibao as Haibao Tang	More...				almost 15 years ago
move global filter before tandems. remove 1e-4 limit.	brentp	More...				almost 15 years ago
add global density filter option.	brentp	More...				almost 15 years ago
make get_order a method on Bed.	brentp	More...				almost 15 years ago
use path of raw file for image.	brentp	More...				almost 15 years ago
fix a small bug: tandem genes are sorted with decreasing size. but when there are ties in the sizes, the sorting is not deterministic. this affects self-self blast. now fixed.	tanghaibao as Haibao Tang	More...				almost 15 years ago
add synteny score	tanghaibao as Haibao Tang	More...				almost 15 years ago
none	tanghaibao as Haibao Tang	More...				almost 15 years ago
remove some residual reference to flat	tanghaibao as Haibao Tang	More...				almost 15 years ago
add synteny region finder in scripts/synteny_score.py	tanghaibao as Haibao Tang	More...				almost 15 years ago
add option not to strip alternative splicing.	brentp	More...				almost 15 years ago
readme	tanghaibao as Haibao Tang	More...				almost 15 years ago
minor in run.sh	tanghaibao as Haibao Tang	More...				almost 15 years ago
Merge branch 'master' of [email protected]:tanghaibao/quota-alignment	brentp	More...				almost 15 years ago
remove Flat stuff from blast_to_raw. explicit path ./ in run.sh	brentp	More...				almost 15 years ago
readme minor change	tanghaibao as Haibao Tang	More...				almost 15 years ago
we want stuff!	brentp	More...				almost 15 years ago
axes labels when bed is send in with a full path.	brentp	More...				almost 15 years ago
put BlastLine into bed_utils	tanghaibao as Haibao Tang	More...				almost 15 years ago
add dotplot scripts blast_plot (similar to qa_plot but works on a blast file)	tanghaibao as Haibao Tang	More...				almost 15 years ago
put brentp's verbose blast datafields back	tanghaibao as Haibao Tang	More...				almost 15 years ago
draw box for qa_plot	tanghaibao as Haibao Tang	More...				almost 15 years ago
when working on self-self, flip (subject, query) in blast_to_raw	tanghaibao as Haibao Tang	More...				almost 15 years ago
minor dot plot fix	tanghaibao as Haibao Tang	More...				almost 15 years ago
use tabs rather than spaces in the bed output for gff_to_bed	tanghaibao as Haibao Tang	More...				almost 15 years ago
handles self-self blast	tanghaibao as Haibao Tang	More...				almost 15 years ago

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