The qmito project seems very draft, it is runnable but the options are ambiguous, documents were very dated. The two modes are totally independent, so we made two sets of usage options. These options are renamed based on our name conversion rule. The document is updated.
Updated tool options for metic mode is shown as below:
usage: java -cp qmito.jar au.edu.qimr.qmito.Metric --output <output> --input <bam file> --reference <reference file> --log <logfile> [options]
Option Description
------ -----------
--help Show usage and help.
--input Req, a SAM/BAM file with full path
--log Req, Log file with full path.
--loglevel (Opt, Logging level [INFO,DEBUG], Def = INFO.
--lowread-count <Integer> (Optional) Specify an integer here. It will report true if the coverage
on that base is lower than this integer.
--mito-name Opt, specify mitochondrial sequence name listed on reference file,
Def=chrMT.
--nonref-threshold <Integer> (Optional) Specify an integer here. It will report true if the non-
reference ratio on that base is higher than this proportion .
--output Req, a full path TSV format file
--query Opt,A string with double quotation, following qbamfilter query rule.
Default query is "and (flag_NotprimaryAlignment == false,
flag_ReadUnmapped == false)"
--reference Req, a reference file with fa format where input BAM files are mapped.
--version Show version number.
Updated tool options for metic mode is shown as below:
usage: java -cp qmito.jar au.edu.qimr.qmito.Stat --output <output> --input-control <control metric input> --input-test <test metric input> --log <logfile> [options]
Option Description
------ -----------
--help Show usage and help.
--input-control Req, a metric file of control sample with tsv format, created by
qmito/qpileup
--input-test a metric file of test sample with tsv format, created by qmito/qpileup
--log Req, Log file with full path.
--loglevel (Opt, Logging level [INFO,DEBUG], Def = INFO.
--output Req, a full path TSV format file
--version Show version number.
Type of change
Please delete options that are not relevant.
[ ] Bug fix (non-breaking change which fixes an issue)
[x] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
[ ] This change requires a documentation update
How Has This Been Tested?
unit test is added and also run on real data.
Are WDL Updates Required?
not required
Checklist:
[X] My code follows the style guidelines of this project
[X] I have performed a self-review of my own code
[X] I have commented my code, particularly in hard-to-understand areas
[X] My changes generate no new warnings
[X] I have added tests that prove my fix is effective or that my feature works
[X] New and existing unit tests pass locally with my changes
Description
The qmito project seems very draft, it is runnable but the options are ambiguous, documents were very dated. The two modes are totally independent, so we made two sets of usage options. These options are renamed based on our name conversion rule. The document is updated.
Updated tool options for metic mode is shown as below:
Updated tool options for metic mode is shown as below:
Type of change
Please delete options that are not relevant.
How Has This Been Tested?
unit test is added and also run on real data.
Are WDL Updates Required?
not required
Checklist: