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100 Open 296 Closed
100 Open 296 Closed
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Issues list

test-collapse-seg1 fails
#441 opened Mar 7, 2025 by diekhans
manifest files should contain paths realtive to the manifiest file, not relative to the current directory. command line Issues related to command line enhancement New feature or request
#440 opened Mar 7, 2025 by diekhans
@diekhans
2
quantify doesn't have an option to take a fasta/fastq, only a manafest command line Issues related to command line enhancement New feature or request mod; quantify
#439 opened Mar 7, 2025 by diekhans
@diekhans
1
flair correct should sort output enhancement New feature or request File I/O File parsing and formatting mod; correct
#438 opened Mar 6, 2025 by diekhans
collapse produce no output on single exon test case bug Something isn't working mod; collapse
#437 opened Mar 6, 2025 by diekhans
@diekhans
invalid flair quantify -r argument is detected but does not error exit Error handling Issues with error handling and logging mod; quantify
#436 opened Mar 6, 2025 by diekhans
@diekhans
flair collapse generates a confusing pysam error when nothing aligned bug Something isn't working Error handling Issues with error handling and logging mod; collapse
#435 opened Mar 6, 2025 by diekhans
@diekhans
3
Memory issues with flair collapse
#432 opened Feb 27, 2025 by linley-sherin
1
falir align should use -x splice:hq for PacBio CCS mod; align
#430 opened Feb 25, 2025 by diekhans
@diekhans
1
Incorrect documentation and defaults on flair-align --filtertype bug Something isn't working command line Issues related to command line mod; align
#427 opened Feb 25, 2025 by diekhans
@diekhans
Filter supplementary alignments when reading BAMs, not prefilter enhancement New feature or request mod; align
#426 opened Feb 25, 2025 by diekhans
3
Unclear about --no_redundant flag Documentation Update ReadTheDocs manual
#425 opened Feb 22, 2025 by linley-sherin
4
Different annotation information with input GTF (flair collapse)
#422 opened Feb 14, 2025 by shin0727
1
Flair collapse error after filtering cov step mod; collapse
#420 opened Feb 14, 2025 by NHoang98 FLAIR 2.1
@diekhans
2
using Flair for novel transcript discovery
#419 opened Feb 12, 2025 by baibhav-bioinfo
7
Depreciate DESeq and DRIMSeq wrapper scripts Documentation Update ReadTheDocs manual enhancement New feature or request mod; diffexp mod; diffsplice mod; quantify
#418 opened Feb 10, 2025 by diekhans FLAIR 2.1
@diekhans
1
output of diff splice is not stable bug Something isn't working mod; diffsplice
#417 opened Feb 6, 2025 by diekhans
minimap2transcriptomeindex.0000.tmp create in current directory rather than run-specific directory
#416 opened Feb 6, 2025 by diekhans FLAIR 2.1
@diekhans
FLAIR 2.1 release
#413 opened Feb 5, 2025 by diekhans
2 of 17 tasks
FLAIR 2.1
@diekhans
1
Improve detection of novel splice sites that minimap alignment misses
#412 opened Feb 4, 2025 by cafelton
work with SQANTi3 to get evaluation result in an easy to parse format.. enhancement New feature or request Testing Testing-related tickets
#411 opened Jan 29, 2025 by diekhans
@diekhans
Running flair collapse with longshot input
#410 opened Jan 22, 2025 by laulambr
3
FLAIR collapse 5'/3' UTR and splice isoform issue bug Something isn't working mod; collapse
#409 opened Jan 21, 2025 by mckalem
3
use argparse in main flair and clean up all argument parsing cleanup Code cleanup and simplification command line Issues related to command line
#408 opened Jan 21, 2025 by diekhans
@diekhans
update development,, pip, docker, pypi, etc building Documentation Update ReadTheDocs manual source install release Issues with source mgt, install, and releases
#407 opened Jan 16, 2025 by diekhans
5 tasks
@diekhans
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