yanghchen perm issues - Githubissues

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unable to generate log file

#55 GoogleCodeExporter opened 9 years ago
0
count.sh

#54 GoogleCodeExporter opened 9 years ago
0
# of reported mapped reads in stdout does not match # of mapped reads in sam file

#53 GoogleCodeExporter opened 9 years ago
1
Reads parsing will quit when encounter reads shorter than expected

#52 GoogleCodeExporter opened 9 years ago
1
The released 0.3.9 source is not compilable

#51 GoogleCodeExporter opened 9 years ago
0
The released 0.3.9 executable are not

#50 GoogleCodeExporter opened 9 years ago
0
The mapping format for paired end read mapping doesn't contain enough information.

#49 GoogleCodeExporter opened 9 years ago
0
Allow 128 x 128 paired-end mapping

#48 GoogleCodeExporter opened 9 years ago
0
Align reads to Null_Region

#47 GoogleCodeExporter opened 9 years ago
1
Error in processing reference genomes with small charater 'n'

#46 GoogleCodeExporter opened 9 years ago
0
SAM to BAM conversion error

#45 GoogleCodeExporter opened 9 years ago
2
Filter reads with given number of 'N'

#44 GoogleCodeExporter opened 9 years ago
0
out put mapped read in fastq foramt

#43 GoogleCodeExporter opened 9 years ago
1
Increase the maximum # of alignments per reads from 2000 to 1 million

#42 GoogleCodeExporter opened 9 years ago
1
Segmentation fault when -m -s Unwritable path

#41 GoogleCodeExporter opened 9 years ago
0
Allowing PerM to map 15 bp reads with seed F1 and 20bp reads with seed F2

#40 GoogleCodeExporter opened 9 years ago
1
Bug with using -k 2 or -k 1 with -a

#39 GoogleCodeExporter opened 9 years ago
4
output format error for fasta input and .mapping output

#38 GoogleCodeExporter opened 9 years ago
0
Clean up various informative messages

#37 GoogleCodeExporter opened 9 years ago
2
The way to deal with ambiguous reads has changed.

#36 GoogleCodeExporter opened 9 years ago
0
Couldn't mapped Illumina reads with length > 64 and odd read length

#35 GoogleCodeExporter opened 9 years ago
0
Limitation of 6 mismatches in SOLiD reads

#34 GoogleCodeExporter opened 9 years ago
0
-u unmapped reads -o outputFile.sam doesn't work dirrectly for multiple reads file！

#33 GoogleCodeExporter opened 9 years ago
1
Unmapped Reads

#32 GoogleCodeExporter opened 9 years ago
0
options for # of substituitons -v for long reads was doubled

#31 GoogleCodeExporter opened 9 years ago
0
Missing some exact match for long reads

#30 GoogleCodeExporter opened 9 years ago
1
Mapping files format, column 7th definition (When -A options is specified to output ALL mapping in threshold)

#29 GoogleCodeExporter opened 9 years ago
0
The last read map to itself is missed.

#28 GoogleCodeExporter opened 9 years ago
0
[deleted issue]

#27 GoogleCodeExporter closed 9 years ago
0
-T options didn't work for reads > 64 bp.

#26 GoogleCodeExporter opened 9 years ago
0
Compiled EXE can't be used in other Computer due to missing library

#25 GoogleCodeExporter opened 9 years ago
1
reads in fasta format is not error tolerent enough

#24 GoogleCodeExporter opened 9 years ago
0
mismatches threshold was set to default -v 3, unchangable, when reading index.

#23 GoogleCodeExporter opened 9 years ago
0
[deleted issue]

#22 GoogleCodeExporter closed 9 years ago
0
[deleted issue]

#21 GoogleCodeExporter closed 9 years ago
0
The filtered reads for long reads (more than 50bp) was wrongly set to 0.

#20 GoogleCodeExporter opened 9 years ago
1
-U and -L was replaced --upperBound and --lowerBound

#19 GoogleCodeExporter opened 9 years ago
0
Read name buffer size was extened from 50 to 100

#18 GoogleCodeExporter closed 9 years ago
0
Unrecognizable are ignored without warning.

#17 GoogleCodeExporter opened 9 years ago
0
Paired-end Mapping

#16 GoogleCodeExporter opened 9 years ago
1
'.' is encoded as 3 without --includeReadsWN

#15 GoogleCodeExporter opened 9 years ago
0
[deleted issue]

#14 GoogleCodeExporter closed 9 years ago
0
Extra blank line at the end of output

#13 GoogleCodeExporter opened 9 years ago
1
Break built for reading the index

#12 GoogleCodeExporter opened 9 years ago
1
The statistics of multiple mapping is not correct when -E is specified.

#11 GoogleCodeExporter opened 9 years ago
0
(1)Can't just find exact matches (2) Extra tab at the end.

#10 GoogleCodeExporter opened 9 years ago
1
Undecided color

#9 GoogleCodeExporter opened 9 years ago
1
Default output file name

#8 GoogleCodeExporter opened 9 years ago
0
Change on default output file name

#7 GoogleCodeExporter opened 9 years ago
2
[deleted issue]

#6 GoogleCodeExporter closed 9 years ago
0