single-end mode is broken in v1.1.0

[niederhuth]

I recently updated my conda installation of pairtools to v1.1.0 and it appears that the --single-end mode no longer works for single-end reads in pairtools parse2:

Comparing two versions:

pairtools 1.0.3 py310hb45ccb3_0 bioconda pairtools 1.1.0 py312hac03d35_1 bioconda

Same command: pairtools parse2 --single-end --nproc-in 12 --nproc-out 32 --min-mapq 1 --flip --add-columns mapq --assembly B73 -c ../ref/B73.chrom_sizes.tsv --output-stats test.tsv -o test.pairs test.input.bam

v1.0.3 gives the expected result, but v1.1.0 reports everything as unmapped:

v.1.10 results are entirely NN: read1 ! 0 ! 0 - - NN 0 0