reformat markdown

Author: gfudenberg

command_line_interface.ipynb

@@ -1,5 +1,13 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "392d13f0",
+   "metadata": {},
+   "source": [
+    "# Command line interface "
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "10e43065",
@@ -766,7 +774,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "0c3184b6",
+   "id": "7445dd23",
    "metadata": {},
    "source": [
     "Punctate pairwise peaks of enriched contact frequency are a prevalent feature of mammalian interphase contact maps.  See the [dots](https://github.com/open2c/open2c_examples/blob/master/dots.ipynb) notebook for more details.\n",
@@ -777,7 +785,7 @@
   {
    "cell_type": "code",
    "execution_count": 19,
-   "id": "25ede2dc",
+   "id": "3718fe1c",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -787,7 +795,7 @@
   {
    "cell_type": "code",
    "execution_count": 20,
-   "id": "0bd99cf2",
+   "id": "29527f75",
    "metadata": {},
    "outputs": [
     {
@@ -1297,7 +1305,7 @@
   {
    "cell_type": "code",
    "execution_count": 21,
-   "id": "060b828b",
+   "id": "d74d206d",
    "metadata": {},
    "outputs": [
     {
@@ -1522,7 +1530,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "31e806a5",
+   "id": "61e68b3b",
    "metadata": {},
    "source": [
     "A common method for quantifying contact maps is by creating pileup plots, which are averages over a set of \"snippets\", or 2D windows, from the genome-wide map. See the [pileups](https://github.com/open2c/open2c_examples/blob/master/pileup_CTCF.ipynb) notebook for more details.\n",
@@ -1533,7 +1541,7 @@
   {
    "cell_type": "code",
    "execution_count": 22,
-   "id": "e08677c3",
+   "id": "6197486f",
    "metadata": {},
    "outputs": [],
    "source": [