BamM
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Ecogenomics
Metagenomics-focused BAM file manipulation
I'm trying to install Bamm from release tag 1.7.3 (https://github.com/Ecogenomics/BamM/archive/1.7.3.tar.gz) on a centos-8.2 system, using gcc/9.2.0 and pythton/2.7.17 I have a compilation error while building libcfu in order to have...
When extracting mapped reads from a bam file, bamm preserves information on read partners between groups by adding a prefix with that information to the extracted read-id. While this feature...
Hi, I am attempting to build BamM for use with GroopM and I am running into an error. This is centos 7. gcc version 4.8.5 20150623 (Red Hat 4.8.5-11) (GCC)...
Is it possible to obtain a summary tsv file showing the number of links between each 2 contigs? Thanks.
I am running the standard install and it is not finding the libcfu/lib folder in the bundle. error from setup.py: checking for libcfu headers in /home/labuser/BamM/c/libcfu-0.03/include... found checking for libcfu...
@minillinim should we list the specific build conditions for v1.7.3. autoconf (v2.68) and automake (v1.11.3)
Hi, I have been trying to install BamM. I am giving it the paths for libraries I needed to install manually. I get this results in the installation process: sudo...
Hello, I am trying to install BamM; however, I got an error. The error message is attached. [install error.txt](https://github.com/Ecogenomics/BamM/files/465924/install.error.txt) Please, let me know what is wrong with me. Thank you....
Since there's so many 0 values in the pileups, given a true coverage of 0.11 and an assumption that no read overlaps another, the tpmean coverage will be 0.01 /...
Hi, When I look at the mapping performance with samtools flagstat I always get a value of 100% for the mapped reads. When I use bwa directly in stead of...
