Change query to indexing

[Phlya]

Fix #143

[agalitsyna]

Fixes also https://github.com/open2c/pairtools/discussions/141

[agalitsyna]

Problems noticed:

• [x] conda does not automatically update the recent release, so we removed it from recommended ways of installation: https://anaconda.org/bioconda/pairtools @golobor may know the ways to fix it
• [x] pip installation requires cython/numpy/pysam for build, so we added it to the docs explicitly

Other changes:

• [X] nose tests substituted with pytest
• [X] small docs update in dedup