pairtools

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single-end mode is broken in v1.1.0

17

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...

niederhuth

What was wrong? - Detection of the read side was not functional with some aligners after API refactoring https://github.com/open2c/pairtools/commit/9d99660ce8ffda66486c2b0cc296a6bb814576bf Technical description of the issue: - Detection of the read side...

agalitsyna

Python 3.13 removes pipes

1

https://github.com/open2c/pairtools/blob/6303de6d9e992e426285840bfd10e7d5dbbc1c84/pairtools/lib/fileio.py#L2 https://docs.python.org/3.13/whatsnew/3.13.html#whatsnew313-pep594 https://docs.python.org/3.13/whatsnew/3.13.html#summary-release-highlights ``` ============================= test session starts ============================== platform linux -- Python 3.13.0rc2, pytest-8.3.2, pluggy-1.5.0 -- /usr/bin/python3.13 cachedir: .pytest_cache rootdir: //.pybuild/cpython3_3.13/build configfile: pytest.ini testpaths: tests plugins: typeguard-4.3.0 collecting ......

stefanor

Phlya

1. CommandFormatter Interface Introduced the CommandFormatter interface, encapsulating file operations and validations.​ Added standard CLI response outputs to enhance user interaction.​ 2. MODES_TO_FILES_PRESET and COMMANDS Configurations (just 2 dicts) MODES_TO_FILES_PRESET:...

Reovirus

Deprecation of `pipes` Module in Python 3.13 in `pairtools/lib/fileio.py`

1

In Python 3.13, the `pipes` module is deprecated and will be removed in future versions of Python. The current implementation in the **`pairtools/lib/fileio.py`** file relies on the `pipes` module, which...

ShigrafS

Modified CLI flags (-c1, -c2, ...) to accept both integers (column in…

1

Closes #264 This PR enhances the flexibility of column specification in `pairtools` by allowing CLI flags (`-c1`, `-c2`, etc.) to accept **both column indices (ints) and column names (strs)**. Additionally,...

ShigrafS

`chrom1`, `chrom2` and `pair_type` fields are now required in pairs file header

3

- Until `v1.0.3`, `pairtools sort` allows the header line to list column names `chr1` and `chr2` (as indicated in [official 4DN specs](https://github.com/4dn-dcic/pairix/blob/master/pairs_format_specification.md?plain=1#L56)). - Starting with `v1.1.0`, `pairtools sort` now expects...

js2264

pairtools:Empty of fully duplicated library, can't estimate complexity

8

Thanks for conducting this useful tool for 3D genome analysis. However, when I tried to convert the bam file (haplotagged by whatshap) to the pairs format, I met the error...

Wong718

Identical read_len1 and read_len2 reported with different real read lengths in R1&2 pairs

5

I have some data with different lengths of read1 (81 nt) and read2 (221 nt) and I want to report the length of the read in the pairs. I add...

Phlya