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itmat
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rum
RNA-Seq Unified Mapper
http://cbil.upenn.edu/RUM
MIT License
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Start a new log file for every invocation of rum_runner align
#90
mdelaurentis
closed
12 years ago
0
Warning message in RUM::JobReport
#89
mdelaurentis
closed
12 years ago
1
Consider making --chunks a required option
#88
mdelaurentis
closed
12 years ago
2
Fix check to make sure user isn't running a job on the head node of PGFI cluster
#87
mdelaurentis
closed
12 years ago
0
Consider making --prefix a required option to rum_indexes
#86
mdelaurentis
closed
12 years ago
0
Get rid of --config option in all documentation
#85
mdelaurentis
closed
12 years ago
0
Indicate which options are required in "rum_runner help align"
#84
mdelaurentis
closed
12 years ago
0
merge_GU_and_TU may output invalid spans
#83
mdelaurentis
closed
12 years ago
0
Allow per-chunk settings
#82
mdelaurentis
opened
12 years ago
0
Handle changed settings better
#81
mdelaurentis
opened
12 years ago
1
Updating run parameters
#80
safisher
closed
12 years ago
6
importing indexes from version 1
#79
safisher
closed
12 years ago
4
argument documentation
#78
safisher
closed
12 years ago
4
Make sure job settings show up in log file
#77
mdelaurentis
closed
12 years ago
1
Missing quantifications of novel exons
#76
mdelaurentis
closed
12 years ago
0
Header missing from junctions_all.rum
#75
mdelaurentis
closed
12 years ago
1
Improve warning message for not enough RAM
#74
mdelaurentis
closed
12 years ago
0
Document --chunk and --process options better
#73
mdelaurentis
closed
12 years ago
0
Document what logging features aren't available if log4perl isn't installed
#72
mdelaurentis
closed
12 years ago
1
Give feedback when a chunk finishes
#71
mdelaurentis
opened
12 years ago
0
Don't kill alignment job if raw read files aren't found
#70
mdelaurentis
closed
12 years ago
1
rum_runner uninitialized value error thrown when no args given.
#69
delagoya
closed
12 years ago
0
Update rum_indexes docs to add --all option
#68
mdelaurentis
closed
12 years ago
0
make_GU_and_GNU suppressing some non-unique mappers
#67
mdelaurentis
closed
12 years ago
0
Handle failed qstat output better
#66
mdelaurentis
closed
12 years ago
1
Add --all option to rum_indexes that install all the indexes
#65
mdelaurentis
closed
12 years ago
1
Don't submit a separate SGE job for postprocessing
#64
mdelaurentis
closed
12 years ago
1
More output during preprocessing
#63
mdelaurentis
closed
12 years ago
4
Make "rum_runner status" auto-refresh
#62
mdelaurentis
opened
12 years ago
0
Restructure indexes
#61
mdelaurentis
closed
12 years ago
1
Decouple binaries from indexes
#60
mdelaurentis
closed
12 years ago
0
Make rum_runner fail if it encounters an unrecognized option
#59
mdelaurentis
closed
12 years ago
0
log level for 2.0.0_11 is debug?
#58
delagoya
closed
12 years ago
1
Fail with nicer error if dependency not found
#57
mdelaurentis
closed
12 years ago
0
Preprocessing restarted when it wasn't necessary
#56
mdelaurentis
closed
12 years ago
0
Data set issue
#55
delagoya
closed
12 years ago
4
Genome size memory calculation still happening even with --ram option
#54
delagoya
closed
12 years ago
1
--preprocessing flag not respectes using --platform SGE
#53
delagoya
closed
12 years ago
4
Improve error reporting for bowtie, blat, mdust
#52
mdelaurentis
closed
12 years ago
0
Error running bowtie on Amazon machine
#51
mdelaurentis
closed
12 years ago
1
Can't run "rum_runner help" from one level up
#50
mdelaurentis
closed
12 years ago
1
SAM file error: alignment start conflicts with reference name
#49
mdelaurentis
closed
12 years ago
4
Problem with yeast index
#48
mdelaurentis
closed
12 years ago
1
Incorrect percentages in mapping_stats_file
#47
mdelaurentis
closed
12 years ago
7
parse_blat_out.pl fails if blat output is empty
#46
mdelaurentis
closed
12 years ago
0
In RUM.sam, QUAL field should be '*' if we don't have quals
#45
mdelaurentis
closed
12 years ago
0
RUM.sam does not contain any information about mismatches
#44
khayer
closed
12 years ago
1
Error with var-length reads if --variable-length-reads option not supplied
#43
mdelaurentis
closed
12 years ago
0
By default, don't log from read-only actions
#42
mdelaurentis
closed
12 years ago
1
Don't log usage mistakes as errors
#41
mdelaurentis
closed
12 years ago
0
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