Add an option to output plot tables.

[xiekunwhy]

Hi,

Would you please add an option to output plain text tables of those in html (including summary table and those for plots), it will be make others easy to incorporate TGSFilter into some pipeline.

Best,
Kun

[HuiyangYu]

Thank you very much for your interest in TGSFilter. In the latest version ( not released) of the software, significant modifications have been made. Your suggestions will be incorporated into the new software release.

[xiekunwhy]

It is not easy to build from source.
mkdir -p /public2/home/sl_qybio/sl_qybio/software/biosoft/TGSFilter/bin
g++ -L/public2/home/sl_qybio/sl_qybio/software/biosoft/TGSFilter/lib --std=c++11 -g -O3 /public2/home/sl_qybio/sl_qybio/software/biosoft/TGSFilter/src/TGSFilter.cpp -lhts -lz -lisal -ldeflate -pthread -fPIE -I/public2/home/sl_qybio/sl_qybio/software/biosoft/TGSFilter/include -o /public2/home/sl_qybio/sl_qybio/software/biosoft/TGSFilter/bin/tgsfilter
/usr/bin/ld: /public2/home/sl_qybio/sl_qybio/software/biosoft/TGSFilter/lib/libisal.a(ec_base.o): unable to initialize decompress status for section .debug_info
/usr/bin/ld: /public2/home/sl_qybio/sl_qybio/software/biosoft/TGSFilter/lib/libisal.a(ec_base.o): unable to initialize decompress status for section .debug_info
/usr/bin/ld: /public2/home/sl_qybio/sl_qybio/software/biosoft/TGSFilter/lib/libisal.a(igzip.o): unable to initialize decompress status for section .debug_info
/usr/bin/ld: /public2/home/sl_qybio/sl_qybio/software/biosoft/TGSFilter/lib/libisal.a(igzip.o): unable to initialize decompress status for section .debug_info
/public2/home/sl_qybio/sl_qybio/software/biosoft/TGSFilter/lib/libisal.a: error adding symbols: File format not recognized
collect2: error: ld returned 1 exit status
make: *** [/public2/home/sl_qybio/sl_qybio/software/biosoft/TGSFilter/bin/tgsfilter] Error 1

[HuiyangYu]

This error is due to the difference of the gcc version between libisal.a under compiled lib and the current environment. These problems will be solved in the latest version. Does the pre-compiled binary program work? If so, you can download and start with the pre-compiled program.

…

---- Replied Message ---- | From | ***@***.***> | | Date | 08/06/2024 14:25 | | To | ***@***.***> | | Cc | Zou ***@***.***>***@***.***> | | Subject | Re: [HuiyangYu/TGSFilter] Add an option to output plot tables. (Issue #1) | It is not easy to build from source. mkdir -p /public2/home/sl_qybio/sl_qybio/software/biosoft/TGSFilter/bin g++ -L/public2/home/sl_qybio/sl_qybio/software/biosoft/TGSFilter/lib --std=c++11 -g -O3 /public2/home/sl_qybio/sl_qybio/software/biosoft/TGSFilter/src/TGSFilter.cpp -lhts -lz -lisal -ldeflate -pthread -fPIE -I/public2/home/sl_qybio/sl_qybio/software/biosoft/TGSFilter/include -o /public2/home/sl_qybio/sl_qybio/software/biosoft/TGSFilter/bin/tgsfilter /usr/bin/ld: /public2/home/sl_qybio/sl_qybio/software/biosoft/TGSFilter/lib/libisal.a(ec_base.o): unable to initialize decompress status for section .debug_info /usr/bin/ld: /public2/home/sl_qybio/sl_qybio/software/biosoft/TGSFilter/lib/libisal.a(ec_base.o): unable to initialize decompress status for section .debug_info /usr/bin/ld: /public2/home/sl_qybio/sl_qybio/software/biosoft/TGSFilter/lib/libisal.a(igzip.o): unable to initialize decompress status for section .debug_info /usr/bin/ld: /public2/home/sl_qybio/sl_qybio/software/biosoft/TGSFilter/lib/libisal.a(igzip.o): unable to initialize decompress status for section .debug_info /public2/home/sl_qybio/sl_qybio/software/biosoft/TGSFilter/lib/libisal.a: error adding symbols: File format not recognized collect2: error: ld returned 1 exit status make: *** [/public2/home/sl_qybio/sl_qybio/software/biosoft/TGSFilter/bin/tgsfilter] Error 1 — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>

[xiekunwhy]

pre-compiled binary program is worked, but the newest version is v1.10, not v1.11.

[MJoseMo]

Hi,

I came across this software on a forum and I would like to ask if this repository has a biorxiv link available to delve into its outputs and representations.

Additionally, I have a question regarding the selection of read type -x argument, particularly distinguish between CLR and Hifi. Many papers mention the methodology of library preparation and kits used. However, I'm unsure how to determine the type of sequencing data (CLR or Hifi). How could I retrieve this kind of information?

[MJoseMo]

I had problems downloading it with building from source section and managed to install it after some changes from pre-built binary section.

Thanks for this tool. I'm looking forward to seeing its outcomes !

 wget -c https://github.com/HuiyangYu/TGSFilter/releases/download/v1.10/TGSFilter-1.10-Linux-x86_64.tar.gz
tar -xzvf TGSFilter-1.10-Linux-x86_64.tar.gz

[MJoseMo]

I would like to ask about the default parameters that are set after selecting different -x options. Did they differ between the possibilities?