{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Sort anyting to anything"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Here is how a classical .pairs file looks like:"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<img src=\"pairs.png\" alt=\".pairs format\" title=\".pairs format\" width=\"400\"/>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "For more details about .pairs file format please look at the [documentation](https://pairtools.readthedocs.io/en/latest/index.html)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "To sort pairs in either the .pairs or .parquet format, you just need to run a simple CLI command (with parameters similar to those used in pairtools).\n",
    "Note that sorting can be combined with conversion - and in most cases, you’ll actually save time by combining processing(in this case sorting) and conversion, rather than performing them separately.\n",
    "\n",
    "Here’s an example with some useful parameters:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "pairs_to_parquet sort -o test_sorted.parquet --nproc 4 --tmpdir /temp_directory --memory 35G test.pairs.gz"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Default option of sorting is to sort pairs by `chr1-chr2-pos1-pos2-pair_type`, where chr and pair_type columns are sorted in `lexicographical` order and pos columns in `numerical` order"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "If you have your own idea, in which order you want to sort you pairs: then you need to specify `c1, c2, p1, p2, pt or even extra_col` parameters"
   ]
  }
 ],
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