Maps base qualities in a BAM file as defined in a base quality mapping file (CSV)
- A BAM file
- A CSV file should contain base quality values as int in the form:
from,to
Requirement: a Nim compiler and the packages:
To compile use: nim c quad.nim
Note: libhts.so needs to be found in your LD_LIBRARY_PATH.
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"
./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
MIT License. See LICENSE file