Martin Mokrejš

I think I saw few times that other tools show short help text with `-h` and verbose help text with `--help`. But I am definitely puzzled why `--usage print this...

What helps to fix the `@RG` line is to use [CTRL+V TAB] instead of writing `\t`. `bowtie2-align-s --rg-id "$flowcell"."$lane"."$sample" --rg "ID:$rgid[CTRL+V TAB]PL:$platform[CTRL+V TAB]LB:$rglb[CTRL+V TAB]PU:$rgpu[CTRL+V TAB]SM:$sample"` But, on alignment lines there...

A workaround is to replace the TAB on alignment lines with a space and drop the unnecessary fields: `sed -e 's/RG:Z:H27CNAFXY.1.xBJ4303[CTRL+V TAB]PL:ILLUMINA[CTRL+V TAB]LB:xBJ4303_ExomABC1_180709[CTRL+V TAB]PU:H27CNAFXY.1[CTRL+V TAB]SM:xBJ4303/RG:Z:H27CNAFXY.1.xBJ4303 SM:xBJ4303/`

> A workaround is to replace the TAB on alignment lines with a space and drop the unnecessary fields: > > `sed -e 's/RG:Z:H27CNAFXY.1.xBJ4303[CTRL+V TAB]PL:ILLUMINA[CTRL+V TAB]LB:xBJ4303_ExomABC1_180709[CTRL+V TAB]PU:H27CNAFXY.1[CTRL+V TAB]SM:xBJ4303/RG:Z:H27CNAFXY.1.xBJ4303 SM:xBJ4303/` But...

> Try this: > `bowtie2-align-s --rg-id "$flowcell"."$lane"."$sample" --rg "ID:$rgid" --rg "PL:$platform" --rg "LB:$rglb" --rg "PU:$rgpu" --rg "SM:$sample"` Right, this ensures `TABs` are used in the `@RG` header line and also,...

More importantly, the specs incidentally say `SM i Template-independent mapping quality` so from that I infer the `SM:xBJ4303` values I added may not appear on the alignment lines, no matter...

@BenLangmead Would you please make a new bowtie1 release with the above patches?

Hi @ch4rr0 , thank you for your efforts. I see https://github.com/gentoo/sci/blob/master/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch is now obsoleted by https://github.com/BenLangmead/bowtie/commit/d8b661fb36c129cb9899fcd3689b3618036f8c7b on the `bug_fixes` branch but unfortunately I cannot compile with even `gcc-8.2.0 -std=c++03`. But...

It installs only README file. And also the downloads in setup.py's CustomBuildCommand() look we want to disable them. But maybe they don't get triggered ... I just thought somebody may...

Well it was a proposal for a new package but I agree it has issues like many biology-oriented tools. Thanks you for your efforts, I understand we are all short...