java -jar /data/results/tools/align/picardtools/picard-tools-1.109/CreateSequenceDictionary.jar R= backbone_wo_insert.fa  O= backbone_wo_insert.dict

@@
java -jar /data/results/tools/align/picardtools/picard-tools-1.109/CreateSequenceDictionary.jar R= /data/results/tools/samtools/samtools-0.1.18/examples/toy.fa  O= /data/results/tools/samtools/samtools-0.1.18/examples/toy.dict
samtools faidx /data/results/tools/samtools/samtools-0.1.18/examples/toy.fa 


cat /data/results/tools/samtools/samtools-0.1.18/examples/toy.sam | java -Xmx500m    -cp "/data/results/tools/align/jvarkit/jvarkit/htsjdk-1.128/dist/commons-jexl-2.1.1.jar:/data/results/tools/align/jvarkit/jvarkit/htsjdk-1.128/dist/commons-logging-1.1.1.jar:/data/results/tools/align/jvarkit/jvarkit/htsjdk-1.128/dist/htsjdk-1.128.jar:/data/results/tools/align/jvarkit/jvarkit/htsjdk-1.128/dist/snappy-java-1.0.3-rc3.jar:/data/results/tools/align/jvarkit/jvarkit/dist-1.128/biostar59647.jar" com.github.lindenb.jvarkit.tools.biostar.Biostar59647  -r /data/results/tools/samtools/samtools-0.1.18/examples/toy.fa /data/results/tools/samtools/samtools-0.1.18/examples/toy.sam ref:9-20 | xmllint --format -

same output:
cat /data/results/tools/samtools/samtools-0.1.18/examples/toy.sam | java -Xmx500m    -cp "/data/results/tools/align/jvarkit/jvarkit/htsjdk-1.128/dist/commons-jexl-2.1.1.jar:/data/results/tools/align/jvarkit/jvarkit/htsjdk-1.128/dist/commons-logging-1.1.1.jar:/data/results/tools/align/jvarkit/jvarkit/htsjdk-1.128/dist/htsjdk-1.128.jar:/data/results/tools/align/jvarkit/jvarkit/htsjdk-1.128/dist/snappy-java-1.0.3-rc3.jar:/data/results/tools/align/jvarkit/jvarkit/dist-1.128/biostar59647.jar" com.github.lindenb.jvarkit.tools.biostar.Biostar59647  -r /data/results/tools/samtools/samtools-0.1.18/examples/toy.fa /data/results/tools/samtools/samtools-0.1.18/examples/toy.sam  | xmllint --format - | wc

@@
cd /data/results/tools/align/jvarkit/jvarkit
make biostar59647
/data/results/tools/align/jvarkit/jvarkit/dist-1.128/biostar59647 --help



java -cp path/to/sam.jar:/path/to/picard.jar:. Biostar59647  \
           ~/samtools-0.1.18/examples/toy.fa \
           ~/samtools-0.1.18/examples/toy.bam \
            ref:9-20 | xmllint --format -



https://www.biostars.org/p/59647/

javac -cp /data/results/tools/align/picardtools/picard-tools-1.109/sam-1.109.jar:/data/results/tools/align/picardtools/picard-tools-1.109/picard-1.109.jar Biostar59647.java

Compilation

to compile a specific tool, say vcffilterjs , type

$ cd jvarkit
$ make vcffilterjs
the required libraries will be downloaded and installed in the dist-XXX directory.

the target 'all' exists in the Makefile but it will generate a large number of tools I don't use/maintain anymore.