zhouqiangwei / dmtools Goto Github PK

Just a quick question about the storage format. Why not include integer counts of methylated reads instead of a float methylation level? The float value storage takes up more file space and could introduce ambiguities due to rounding that would prevent modeling the WGBS data using count models. Thanks!

I would like to express my appreciation for the outstanding functionality provided by the DNA Methylation tools, which have proven to be an invaluable resource in terms of both space and time efficiency.

I kindly request an enhancement to the tool's functionality by adding support for NOMe-seq, specifically for WCG and GCH contexts. Incorporating support for WCG and GCH during the format conversion process would greatly enhance the tool's versatility and utility.

NOMe-Seq is a single-molecule, high-resolution nucleosome positioning assay. This method is based on the ability of the GpC methyltransferase M.CviPI to methylate GpC sites that are not bound by nucleosomes, to create a digital footprint of nucleosome positioning. M.CviPI can map nucleosome positions at CpG-poor promoters, irrespective of their endogenous methylation status. In this method, native chromatin is treated with M.CviPI, following which the DNA is treated with sodium bisulfite and subjected to WGBS. From these data, CpG methylation patterns as well as nucleosome-free regions (GpC methylation) can be identified.1

I would like to extend my gratitude to the developers for their excellent work on this tool, and I look forward to the possibility of seeing NOMe-seq support integrated into future releases.

Thank you for your time and consideration.

After processing all chromosomes, the bam2dm tool in version 0.1.8 of dmtools is causing a memory leak and resulting in a core dump. The logs indicate the following:

[DM::calmeth] Free mem in Methy_List
[DM::calmeth] Free mem in chromsUse
[DM::calmeth] Free mem in all others

*** Error in `/datd/software/GitHub/dmtools-0.1.8/bam2dm': free(): invalid pointer: 0x0000000105096130 ***
======= Backtrace: =========
/usr/lib64/libc.so.6(+0x81329)[0x2ba72083d329]
/datd/software/GitHub/dmtools-0.1.8/bam2dm[0x405061]
/datd/software/GitHub/dmtools-0.1.8/bam2dm[0x406a16]
/usr/lib64/libc.so.6(__libc_start_main+0xf5)[0x2ba7207de555]
/datd/software/GitHub/dmtools-0.1.8/bam2dm[0x407438]
======= Memory map: ========
00400000-004c1000 r-xp 00000000 08:31 126752248867 /datd/software/GitHub/dmtools-0.1.8/bam2dm
006c0000-006c1000 r--p 000c0000 08:31 126752248867 /datd/software/GitHub/dmtools-0.1.8/bam2dm
006c1000-006c2000 rw-p 000c1000 08:31 126752248867 /datd/software/GitHub/dmtools-0.1.8/bam2dm

Environment:
Operating System: Linux mgt 3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 GNU/Linux
dmtools Version: 0.1.8
GNU Make 4.3
g++ (GCC) 11.1.0

If it would facilitate the resolution process, I am available on WeChat for further discussion.