ssadedin bazam issues - Githubissues

ssadedin / bazam

A read extraction and realignment tool for next generation sequencing data

GNU Lesser General Public License v2.1

98 stars 16 forks source link

issues

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Same output for all regions

#34 soumyarao86 opened 1 year ago
0
No output for low-coverage bam files

#33 Npaffen opened 1 year ago
0
locating pairs in CRAM stopped working in versions after 1.0.1

#32 seru71 opened 1 year ago
1
Swapping first and second mates when pair aligned to reverse strand

#31 mikisvaz opened 3 years ago
0
Build failed

#30 Fred-07 opened 3 years ago
0
Realignment to new ref needs recalibration?

#29 TnakaNY opened 3 years ago
0
Issue with build

#28 caleblareau opened 3 years ago
6
common use case - properly paired mates only

#27 benbfly opened 4 years ago
0
cram input

#26 zhangguy closed 4 years ago
0
feature request - colorspace reversion

#25 berntpopp opened 4 years ago
0
feature request - single ended nanopore reads

#24 colindaven opened 4 years ago
0
[feature request?] unmapped with -L 0:0*-0 / skip some reads sorted bam

#23 evolighting opened 5 years ago
0
Unable to access jarfile build/libs/bazam.jar

#22 ehsanullah83 closed 5 years ago
1
-L chr1 runs but does not output anything

#21 bwlang opened 5 years ago
1
-bam is a required parameter

#20 PriitPaluoja opened 5 years ago
0
Option to emit original quality scores in BQSR-ed BAMs

#19 wengkhong closed 5 years ago
4
Inappropriate call if not paired read

#18 ziaursani opened 5 years ago
2
samtools view -bSu in pipe is now redundant

#17 tseemann opened 5 years ago
1
Reference MD5 mismatch for slice 2

#16 YaCui opened 5 years ago
3
Missing Reads

#15 christopher-schroeder opened 5 years ago
2
Compressed output

#14 BrianLohman opened 5 years ago
1
How large memory needed?

#13 simoncchu closed 5 years ago
9
remove reads that are mapped close each other

#12 wsuplantpathology opened 5 years ago
2
Does it work for Bam files where sequences have been removed?

#11 kvittingseerup opened 5 years ago
0
Get BAM or SAM output from tool?

#10 cmdcolin opened 5 years ago
1
OutOfMemoryError

#9 brentp opened 5 years ago
2
how to run on CRAM

#8 brentp closed 5 years ago
3
Now on bioconda

#7 tseemann closed 5 years ago
1
Now in homebrew

#6 tseemann closed 5 years ago
1
--help returns error exit code

#5 tseemann closed 5 years ago
2
WARNING: An illegal reflective access operation has occurred

#4 tseemann closed 5 years ago
8
Needs --version flag

#3 tseemann closed 5 years ago
2
update link for advanced example in README

#2 taylorreiter closed 5 years ago
2
Update link to Bazam-in-STRetch example

#1 hdashnow closed 5 years ago
0