genome bam-readcount issues

genome / bam-readcount

Count bases in BAM/CRAM files

MIT License

298 stars 95 forks source link

issues

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NUL (\x00, ^@) and other control characters in output

#107 Kaddea opened 2 months ago
4
conda version different than github

#106 complexgenome closed 10 months ago
1
Questionably long runtime for RNA BAMs vs. DNA BAMs?

#105 seetarajpara closed 1 year ago
0
Interpretation of indels

#104 sakshamphul closed 1 year ago
2
read depth incorrect

#103 bioscienceresearch closed 2 years ago
2
Compilation Issue

#102 KevinYie opened 2 years ago
3
Reported depth not matching

#101 jcgrenier closed 2 years ago
6
Issue on installation

#100 idoit4fun opened 2 years ago
0
fatal error: compilation failed

#99 smoretti opened 2 years ago
1
Identify reads aligned to mutant and wild type sequences

#98 rpauly closed 2 years ago
1
Badge

#97 sridhar0605 closed 2 years ago
0
`bam-readcount` build from release source code zip/tarball does not have a version number

#96 apldx opened 2 years ago
0
Unix conv help message edits

#95 sridhar0605 closed 2 years ago
0
help message edits

#94 sridhar0605 closed 2 years ago
0
Version and Author contri patch

#93 sridhar0605 closed 2 years ago
0
how to get the site list for indels?

#92 breezetown opened 2 years ago
3
Add tutorial

#91 apldx closed 2 years ago
0
how to get a region file

#90 stroke1989 closed 2 years ago
3
Support for BAM CSI index

#89 f-huber closed 2 years ago
1
Error when path_to_bam have bam in middle

#88 sssimonyang opened 2 years ago
0
Inconsistent output

#87 mnshgl0110 opened 2 years ago
2
WARNING

#86 stroke1989 closed 2 years ago
3
Reason for low coverage output for deepseq data

#85 YashaNazirB opened 2 years ago
5
[JOSS REVIEW] Any functionality documentation?

#84 bebatut closed 2 years ago
2
[JOSS REVIEW] Missing the community contribution guidelines

#83 bebatut closed 2 years ago
2
[JOSS REVIEW] minor edits to the manuscript

#82 friedue closed 2 years ago
3
[JOSS REVIEW] Minor edits to the github-based documentation

#81 friedue opened 2 years ago
3
[JOSS REVIEW] Example usage

#80 friedue closed 2 years ago
6
[JOSS REVIEW] docker documentation

#79 friedue closed 2 years ago
3
compilation failed

#78 lmanchon opened 3 years ago
5
Make Error for boost on MacOS

#77 chintan-vora-tfs opened 3 years ago
4
Move Docker docs to top of README

#76 apldx closed 3 years ago
0
Compilation fails because of missing -fPIC

#75 SethosII closed 3 years ago
2
Add Docker and clean up

#74 apldx closed 3 years ago
0
Samtools 1.10

#73 seqfu closed 3 years ago
1
Only counting multiple aligned reads for one chromosome with "-l *.bed" and "-q 0" parameters

#72 Adglink opened 3 years ago
5
fpfilter.pl - failed to get readcounts for variant allele

#71 Souzavgp opened 3 years ago
0
Fail to open BAM file –q

#70 Souzavgp closed 3 years ago
3
Max depth 8000

#69 LauraVP1994 closed 2 years ago
1
Getting the read names/ IDs?

#68 ghost opened 4 years ago
4
Distance to both 5' and 3' ends

#67 matnguyen opened 4 years ago
0
Is there a recommended citation for this tool?

#66 whtns closed 4 years ago
1
Update included samtools and boost

#65 serge2016 opened 4 years ago
3
Run without errors but failed to produce the site list

#64 drtamermansour opened 5 years ago
8
missing avg_distance_to_effective_3p_end

#63 stemangiola opened 5 years ago
0
Feature request: Request for unmapped region option

#62 ankit4035 opened 5 years ago
2
fail to load bam index

#61 mcfog1 closed 5 years ago
0
make test fails RunBamReadcount (python vs python2)

#60 darked89 opened 5 years ago
0
Update bioconda deployment to Python3.7

#59 MatthewPorterGN opened 5 years ago
2
print-individual-mapq not working

#58 fkokocinski opened 5 years ago
2