mafTools
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dentearl
Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.
Hi ! Because I divided the chromosomes for lastZ
Hello, For a given input MAF file I would like to list the coverage for binned genomic regions based on the reference sequence. 'mafCoverage' seems to be promising however it...
Hello, I guess the `mafStats` bundled in the Cactus installation (2.3.0) is from mafTools. :) If so, I have a few questions on how to read the results: 1. Is...
Hi, The overall MAF file was obtained based on 10 genomes comparison, I want to find the regions that satisfy the conditions: highly similar in Sample1, Sample2, Sample3 and no...
Hi, I'm having a problem compiling mafToFastaStitcher. I'm getting this error ``` src/mafToFastaStitcherAPI.c:655:22: error: ‘%lu’ directive writing between 1 and 19 bytes into a region of size 7 [-Werror=format-overflow=] sprintf(fmtName,...
(I'm not expecting any response, as this package hasn't been modified in ten years. But I'm recording this issue in case anyone picks up this package in the future.) I'm...
Hello I am running mafToFastaStitcher command with test data: `/data/01/p1/user157/software/mafTools/bin/mafToFastaStitcher -m input.maf --seqs input.fa --breakpointPenalty 5 --outMfa output.mfa` The input.maf is: ``` ## maf version=1 a score=0.0 `status=test.input` s ref.chr1...
Hi, I met errors when installed mafToFastaStitcher like this: `cd mafToFastaStitcher && make all make[1]: Entering directory '/workspace/home/pig/wangdd/maf/mafTools/mafToFastaStitcher' gcc -std=c99 -Wno-unused-but-set-variable -c src/mafToFastaStitcherAPI.c -o src/mafToFastaStitcherAPI.o.tmp -O3 -Wall -Werror --pedantic -funroll-loops...
