Gabriel Renaud
Gabriel Renaud
I would like this issue reopened, even when I specify the --num-threads to say 4, it still takes all of the cores available.
ok I left it to run, it maxes out to the maximum CPU and then writes "finished decompress" then goes down to 4 cores. Any chance it could be capped...
Hello! I am using command line options as such without config.yaml: `Rscript ~/miniconda2/pkgs/r-ichorcna-0.2.0-r36_0/bin/runIchorCNA.R --id myid --WIG input.wig --ploidy "c(2,3)" --normal "c(0.5,0.6,0.7,0.8,0.9)" --maxCN 5 --gcWig [path]/gc_hg19_1000kb.wig --mapWig [path]/map_hg19_1000kb.wig --centromere [path]/GRCh37.p13_centromere_UCSC-gapTable.txt --normalPanel...
I downloaded kalign_v3.4.0 and ran: ``` mkdir build cd build /path/Software/cmake/cmake-3.28.3-linux-x86_64/bin/cmake .. #this is because my system cmake was too "old" ``` this worked then I did: `make` this stopped...
I managed to compile by copy-pasting: #include "version.h" #define KALIGN_PACKAGE_NAME "kalign" #define KALIGN_PACKAGE_VERSION "3.4.0" into msa_io.c and test.c but that is not pretty :-)
Hi Derek ! Thanks for your reply. Yes the message above is decommpressed and piped into xxd.
That would be great ! I understand when we read SAM, it is impossible to tell whether the quality field is empty but this is via C++ code and we...
yeah we deal with ancient DNA and we can end up with really tiny sequences.
Also with the ability to keep QC failed flags in the bam file.
I second this enhancement.