@jbrowse/cli 2.9.0 → 2.10.0

package/README.md

@@ -54,6 +54,7 @@ It is likely preferable in most cases to install the tools globally with
 - [`jbrowse admin-server`](#jbrowse-admin-server)
 - [`jbrowse create LOCALPATH`](#jbrowse-create-localpath)
 - [`jbrowse help [COMMANDS]`](#jbrowse-help-commands)
+- [`jbrowse make-pif FILE`](#jbrowse-make-pif-file)
 - [`jbrowse remove-track TRACK`](#jbrowse-remove-track-track)
 - [`jbrowse set-default-session`](#jbrowse-set-default-session)
 - [`jbrowse sort-gff FILE`](#jbrowse-sort-gff-file)
@@ -204,7 +205,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.9.0/products/jbrowse-cli/src/commands/add-assembly.ts)_
+[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.0/products/jbrowse-cli/src/commands/add-assembly.ts)_
 
 ## `jbrowse add-connection CONNECTIONURLORPATH`
 
@@ -255,7 +256,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.9.0/products/jbrowse-cli/src/commands/add-connection.ts)_
+[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.0/products/jbrowse-cli/src/commands/add-connection.ts)_
 
 ## `jbrowse add-track TRACK`
 
@@ -336,7 +337,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.9.0/products/jbrowse-cli/src/commands/add-track.ts)_
+[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.0/products/jbrowse-cli/src/commands/add-track.ts)_
 
 ## `jbrowse add-track-json TRACK`
 
@@ -366,7 +367,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.9.0/products/jbrowse-cli/src/commands/add-track-json.ts)_
+[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.0/products/jbrowse-cli/src/commands/add-track-json.ts)_
 
 ## `jbrowse admin-server`
 
@@ -398,7 +399,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.9.0/products/jbrowse-cli/src/commands/admin-server.ts)_
+[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.0/products/jbrowse-cli/src/commands/admin-server.ts)_
 
 ## `jbrowse create LOCALPATH`
 
@@ -455,7 +456,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.9.0/products/jbrowse-cli/src/commands/create.ts)_
+[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.0/products/jbrowse-cli/src/commands/create.ts)_
 
 ## `jbrowse help [COMMANDS]`
 
@@ -478,6 +479,36 @@ DESCRIPTION
 _See code:
 [@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v5.2.20/src/commands/help.ts)_
 
+## `jbrowse make-pif FILE`
+
+creates pairwise indexed PAF (PIF), with bgzip and tabix
+
+```
+USAGE
+  $ jbrowse make-pif FILE [--out <value>] [--csi] [-h]
+
+ARGUMENTS
+  FILE  PAF file as input
+
+FLAGS
+  -h, --help         Show CLI help.
+      --csi          Create a CSI index for the PIF file instead of TBI
+      --out=<value>  Where to write the output file. will write ${file}.pif.gz and ${file}.pif.gz.tbi
+
+DESCRIPTION
+  creates pairwise indexed PAF (PIF), with bgzip and tabix
+
+EXAMPLES
+  $ jbrowse pif input.paf # creates input.pif.gz in same directory
+
+
+
+  $ jbrowse pif input.paf --out output.pif.gz # specify output file, creates output.pif.gz.tbi also
+```
+
+_See code:
+[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.0/products/jbrowse-cli/src/commands/make-pif.ts)_
+
 ## `jbrowse remove-track TRACK`
 
 Remove a track configuration from a JBrowse 2 configuration. Be aware that this
@@ -504,7 +535,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.9.0/products/jbrowse-cli/src/commands/remove-track.ts)_
+[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.0/products/jbrowse-cli/src/commands/remove-track.ts)_
 
 ## `jbrowse set-default-session`
 
@@ -543,7 +574,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.9.0/products/jbrowse-cli/src/commands/set-default-session.ts)_
+[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.0/products/jbrowse-cli/src/commands/set-default-session.ts)_
 
 ## `jbrowse sort-gff FILE`
 
@@ -553,11 +584,14 @@ sort and grep
 
 ```
 USAGE
-  $ jbrowse sort-gff FILE
+  $ jbrowse sort-gff FILE [-h]
 
 ARGUMENTS
   FILE  GFF file
 
+FLAGS
+  -h, --help  Show CLI help.
+
 DESCRIPTION
   Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by
   refname and start position using unix utilities sort and grep
@@ -571,7 +605,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.9.0/products/jbrowse-cli/src/commands/sort-gff.ts)_
+[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.0/products/jbrowse-cli/src/commands/sort-gff.ts)_
 
 ## `jbrowse text-index`
 
@@ -638,7 +672,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.9.0/products/jbrowse-cli/src/commands/text-index.ts)_
+[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.0/products/jbrowse-cli/src/commands/text-index.ts)_
 
 ## `jbrowse upgrade [LOCALPATH]`
 
@@ -701,7 +735,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.9.0/products/jbrowse-cli/src/commands/upgrade.ts)_
+[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.10.0/products/jbrowse-cli/src/commands/upgrade.ts)_
 
 <!-- commandsstop -->
 

package/lib/commands/add-track.js

@@ -90,6 +90,7 @@ class AddTrack extends base_1.default {
         });
         if ([
             'PAFAdapter',
+            'PairwiseIndexedPAFAdapter',
             'DeltaAdapter',
             'ChainAdapter',
             'MashMapAdapter',
@@ -97,6 +98,7 @@ class AddTrack extends base_1.default {
             'MCScanSimpleAnchorsAdapter',
         ].includes(adapter.type)) {
             // @ts-expect-error
+            // this is for the adapter's assembly names
             adapter.assemblyNames = assemblyNames.split(',').map(a => a.trim());
         }
         if (isUrl(location) && load) {
@@ -206,7 +208,8 @@ class AddTrack extends base_1.default {
         }
         else if (/\.gff3?\.b?gz$/i.test(location) ||
             /\.vcf\.b?gz$/i.test(location) ||
-            /\.bed\.b?gz$/i.test(location)) {
+            /\.bed\.b?gz$/i.test(location) ||
+            /\.pif\.b?gz$/i.test(location)) {
             return {
                 file: location,
                 index: index || `${location}.tbi`,
@@ -320,6 +323,16 @@ class AddTrack extends base_1.default {
                 bedLocation: makeLocation(location),
             };
         }
+        else if (/\.pif\.b?gz$/i.test(location)) {
+            return {
+                type: 'PairwiseIndexedPAFAdapter',
+                pifGzLocation: makeLocation(location),
+                index: {
+                    location: makeLocation(index || `${location}.tbi`),
+                    indexType: index?.toUpperCase().endsWith('CSI') ? 'CSI' : 'TBI',
+                },
+            };
+        }
         else if (/\.bed\.b?gz$/i.test(location)) {
             return {
                 type: 'BedTabixAdapter',
@@ -447,6 +460,7 @@ class AddTrack extends base_1.default {
             DeltaAdapter: 'SyntenyTrack',
             ChainAdapter: 'SyntenyTrack',
             MashMapAdapter: 'SyntenyTrack',
+            PairwiseIndexedPAFAdapter: 'SyntenyTrack',
             MCScanAnchorsAdapter: 'SyntenyTrack',
             MCScanSimpleAnchorsAdapter: 'SyntenyTrack',
         };

package/lib/commands/make-pif.js

@@ -0,0 +1,117 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.createPIF = exports.swapIndelCigar = exports.flipCigar = void 0;
+const fs_1 = __importDefault(require("fs"));
+const readline_1 = __importDefault(require("readline"));
+const zlib_1 = require("zlib");
+const core_1 = require("@oclif/core");
+const command_exists_1 = require("command-exists");
+const child_process_1 = require("child_process");
+const path_1 = __importDefault(require("path"));
+const base_1 = __importDefault(require("../base"));
+const cigarRegex = new RegExp(/([MIDNSHPX=])/);
+function getReadline(filename) {
+    const stream = fs_1.default.createReadStream(filename);
+    return readline_1.default.createInterface({
+        input: filename.match(/.b?gz$/) ? stream.pipe((0, zlib_1.createGunzip)()) : stream,
+    });
+}
+function getStdReadline() {
+    return readline_1.default.createInterface({
+        input: process.stdin,
+    });
+}
+function parseCigar(cigar = '') {
+    return cigar.split(cigarRegex).slice(0, -1);
+}
+function flipCigar(cigar) {
+    const arr = [];
+    for (let i = cigar.length - 2; i >= 0; i -= 2) {
+        arr.push(cigar[i]);
+        const op = cigar[i + 1];
+        if (op === 'D') {
+            arr.push('I');
+        }
+        else if (op === 'I') {
+            arr.push('D');
+        }
+        else {
+            arr.push(op);
+        }
+    }
+    return arr;
+}
+exports.flipCigar = flipCigar;
+function swapIndelCigar(cigar) {
+    return cigar.replaceAll('D', 'K').replaceAll('I', 'D').replaceAll('K', 'I');
+}
+exports.swapIndelCigar = swapIndelCigar;
+async function createPIF(filename, stream) {
+    const rl1 = filename ? getReadline(filename) : getStdReadline();
+    for await (const line of rl1) {
+        const [c1, l1, s1, e1, strand, c2, l2, s2, e2, ...rest] = line.split('\t');
+        stream.write([`t${c2}`, l2, s2, e2, strand, c1, l1, s1, e1, ...rest].join('\t') + '\n');
+        const cigarIdx = rest.findIndex(f => f.startsWith('cg:Z'));
+        const CIGAR = rest[cigarIdx];
+        if (CIGAR) {
+            rest[cigarIdx] = `cg:Z:${strand === '-'
+                ? flipCigar(parseCigar(CIGAR.slice(5))).join('')
+                : swapIndelCigar(CIGAR.slice(5))}`;
+        }
+        stream.write([`q${c1}`, l1, s1, e1, strand, c2, l2, s2, e2, ...rest].join('\t') + '\n');
+    }
+    rl1.close();
+}
+exports.createPIF = createPIF;
+class MakePIF extends base_1.default {
+    async run() {
+        const { args: { file }, flags: { out, csi }, } = await this.parse(MakePIF);
+        if ((0, command_exists_1.sync)('sh') &&
+            (0, command_exists_1.sync)('sort') &&
+            (0, command_exists_1.sync)('grep') &&
+            (0, command_exists_1.sync)('tabix') &&
+            (0, command_exists_1.sync)('bgzip')) {
+            const fn = out || `${path_1.default.basename(file || 'output', '.paf')}.pif.gz`;
+            const child = (0, child_process_1.spawn)('sh', [
+                '-c',
+                `sort -t"\`printf '\t'\`" -k1,1 -k3,3n | bgzip > ${fn}; tabix ${csi ? '-C ' : ''}-s1 -b3 -e4 -0 ${fn}`,
+            ], {
+                env: { ...process.env, LC_ALL: 'C' },
+                stdio: ['pipe', process.stdout, process.stderr],
+            });
+            await createPIF(file, child.stdin);
+            child.stdin.end();
+            await new Promise(resolve => {
+                child.on('close', resolve);
+            });
+        }
+        else {
+            throw new Error('Unable to sort, requires unix type environment with sort, grep, bgzip, tabix');
+        }
+    }
+}
+MakePIF.description = 'creates pairwise indexed PAF (PIF), with bgzip and tabix';
+MakePIF.examples = [
+    '$ jbrowse pif input.paf # creates input.pif.gz in same directory',
+    '',
+    '$ jbrowse pif input.paf --out output.pif.gz # specify output file, creates output.pif.gz.tbi also',
+];
+MakePIF.flags = {
+    out: core_1.Flags.string({
+        description: 'Where to write the output file. will write ${file}.pif.gz and ${file}.pif.gz.tbi',
+    }),
+    csi: core_1.Flags.boolean({
+        description: 'Create a CSI index for the PIF file instead of TBI',
+    }),
+    help: core_1.Flags.help({ char: 'h' }),
+};
+MakePIF.args = {
+    file: core_1.Args.string({
+        required: true,
+        description: `PAF file as input`,
+    }),
+};
+exports.default = MakePIF;

package/lib/commands/sort-gff.js

@@ -39,4 +39,7 @@ SortGff.args = {
         description: `GFF file`,
     }),
 };
+SortGff.flags = {
+    help: core_1.Flags.help({ char: 'h' }),
+};
 exports.default = SortGff;

package/oclif.manifest.json

@@ -684,6 +684,57 @@
         "create.js"
       ]
     },
+    "make-pif": {
+      "aliases": [],
+      "args": {
+        "file": {
+          "description": "PAF file as input",
+          "name": "file",
+          "required": true
+        }
+      },
+      "description": "creates pairwise indexed PAF (PIF), with bgzip and tabix",
+      "examples": [
+        "$ jbrowse pif input.paf # creates input.pif.gz in same directory",
+        "",
+        "$ jbrowse pif input.paf --out output.pif.gz # specify output file, creates output.pif.gz.tbi also"
+      ],
+      "flags": {
+        "out": {
+          "description": "Where to write the output file. will write ${file}.pif.gz and ${file}.pif.gz.tbi",
+          "name": "out",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "csi": {
+          "description": "Create a CSI index for the PIF file instead of TBI",
+          "name": "csi",
+          "allowNo": false,
+          "type": "boolean"
+        },
+        "help": {
+          "char": "h",
+          "description": "Show CLI help.",
+          "name": "help",
+          "allowNo": false,
+          "type": "boolean"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "make-pif",
+      "pluginAlias": "@jbrowse/cli",
+      "pluginName": "@jbrowse/cli",
+      "pluginType": "core",
+      "strict": true,
+      "isESM": false,
+      "relativePath": [
+        "lib",
+        "commands",
+        "make-pif.js"
+      ]
+    },
     "remove-track": {
       "aliases": [],
       "args": {
@@ -842,7 +893,15 @@
         "$ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz",
         "$ tabix sorted.gff.gz"
       ],
-      "flags": {},
+      "flags": {
+        "help": {
+          "char": "h",
+          "description": "Show CLI help.",
+          "name": "help",
+          "allowNo": false,
+          "type": "boolean"
+        }
+      },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
       "id": "sort-gff",
@@ -1087,5 +1146,5 @@
       ]
     }
   },
-  "version": "2.9.0"
+  "version": "2.10.0"
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/cli",
-  "version": "2.9.0",
+  "version": "2.10.0",
   "description": "A command line tool for working with JBrowse 2",
   "keywords": [
     "jbrowse",
@@ -75,5 +75,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "a50b6f67cf8c8f3c65a7b8cd858de2fcca1f2909"
+  "gitHead": "223d8bfb68fd1bacaf22852639ad5920f1b7f43b"
 }