Maps base qualities in a BAM file as defined in a base quality mapping file (CSV)

Input

1. A BAM file
2. A CSV file should contain base quality values as int in the form: from,to

Compilation

Requirement: a Nim compiler and the packages:

• hts
• csvtools
• cligen

To compile use: nim c quad.nim

Note: libhts.so needs to be found in your LD_LIBRARY_PATH.

Binaries

To avoid the hassle of compilation altogether, use the statically compiled binary (Linux only), provided in the release packages.

Binaries were built with Brent Pedersen's hts_nim_static_builder:

hts_nim_static_builder -s quad --deps "hts@>=0.3.23" --deps "cligen@>=1.4.1" --deps "csvtools@>=0.2.1"

Example execution

./quad -q example/qmap_even2.csv -i example/Col0_C1.100k.bam -o out.bam

When stdout (-) is used for output the format changes automatically to SAM. The output format can be changed with --out-fmt

License

MIT License. See LICENSE file