lindenb
commented
1 year ago It's available in the dev branch of jvarkit:
$ java -jar dist/jvarkit.jar sortsamrefname -h
Usage: sortsamrefname [options] Files
Options:
--bamcompression
Compression Level. 0: no compression. 9: max compression;
Default: 5
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
--maxRecordsInRam
When writing files that need to be sorted, this will specify the number
of records stored in RAM before spilling to disk. Increasing this number
reduces the number of file handles needed to sort a file, and increases
the amount of RAM needed
Default: 50000
-o, --out
Output file. Optional . Default: stdout
-R, --reference
Indexed fasta Reference file. This file must be indexed with samtools
faidx and with picard CreateSequenceDictionary
--regions
Limit analysis to this interval. A source of intervals. The following
suffixes are recognized: vcf, vcf.gz bed, bed.gz, gtf, gff, gff.gz,
gtf.gz.Otherwise it could be an empty string (no interval) or a list of
plain interval separated by '[ \t\n;,]'
--samoutputformat
Sam output format.
Default: SAM
Possible Values: [BAM, SAM, CRAM]
--tmpDir
tmp working directory. Default: java.io.tmpDir
Default: []
--validation-stringency
SAM Reader Validation Stringency
Default: LENIENT
Possible Values: [STRICT, LENIENT, SILENT]
--version
print version and exit
Leo-ccc
Verify
Subject of the issue
Task 'sortsamrefname' not found in root project 'jvarkit'.
Your environment
${JAVA_HOME}/work/my-account/miniconda3Steps to reproduce
./gradlew sortsamrefname
Expected behaviour
Tell us what should happen
Actual behaviour
FAILURE: Build failed with an exception.
What went wrong: Task 'sortsamrefname' not found in root project 'jvarkit'.
Try:
Get more help at https://help.gradle.org
Thank you!