Benjamin Langmead

You are correct that "name" means the whole name, not truncating at the first space. It is common for FASTQ files to have read names with spaces (as you show),...

Are you using `--local` to align? Please share the entire alignment command. Also, note that the `M` CIGAR operation means _either_ match or mismatch. So that CIGAR string is compatible...

I think the issue is that `--end-to-end` mode will not align a read to a reference sequence that is shorter than the read. Soft clipping is needed. If you'd like...

Could you try making one slight change? I think your `--score-min` is changing the constant term but not the coefficient in the minimum score function. So the coefficient is being...

Should have clarified: all the fixes here affect `-r` mode only

I'm unsure where `--no-discordant` enters into this particular issue. When I run those reads through using: ``` bowtie2 -x CBS_pEZY3.fa -1 test_insert0.R1.fq -2 test_insert0.R2.fq ``` I get mostly concordant alignments,...

Could you supply an example so that we can try to reproduce this? We would need the reads, the reference sequence you're aligning to, and the exact command you used.

This makes sense to me, since `bowtie2`, `bowtie2-build` and `bowtie2-inspect` are wrapper scripts that do very little themselves except format arguments for the underlying binaries. The binaries end in `-s`...

I am guessing this happens because the conda build process does not include the `VERSION` file, which the `Makefile` attempts to `cat` into the `BOWTIE2_VERSION` macro, but I will defer...

Thank you Kevin! Extremely helpful, @ch4rr0 and I will take a look. Hopefully we can close that older issue you referenced (#38) as well.