post-v1.0.0 proposals and issues (header post)

[agalitsyna]

Needs discussion/fix:

• bam annotation? add extra pair-related annotation to bams, which would allow to restore .pairs from annotated bams #67
• report mapq in the stats: collect mapq stats in the pairs-stats if possible #80 (or extend to any specified additional fields?) This was actually implemented in the 1.0.0 release...
• support Python 3.10: not possible due to conda problem with glibc
• single-cell walkthrough: too detailed
• more extended description of pair types standards, maybe a walkthrough (see question: total_single_sided_mapped contains Pair types #112, also Fragment-level analysis #68, type of UU (unique-unique) is close to each other #104)
• Add tests for compression-decompression: add tests for compression/decompression #51
• Add tests for example_pipeline @golobor : add a test for the example_pipeline #35
• Line split fix for non-pysam parsers: IndexError in pairtools split  #145

Postponed but might require discussion.fix at some point:

• duplicate the data processing history (currently stored in @pg fields) in #command fields of the .pairs header:, declined for now: duplicate the data processing history (currently stored in @PG fields) in #command fields of the .pairs header #70
• suggestion to set the default temporary folder to ./ instead of $TMPDIR, declined for now PairTools sort failure on merged data #84
• sort is parallel, but someone reported that it is not for their case, no reproducible example: pairtools sort not parallelizing #72
• pairtools subsampling is present, not clear what might be the modifications: pairsamtools subsampling [new tool, enhancement] #66
• unified way of changing the separator, not clear why it's needed and what are the use cases: in all pairsamtools, have a unified way to provide/override column indices and the separator #50