├── LICENSE ├── README.md ├── Snakefile ├── config.json ├── docs └── README.md ├── scripts ├── mean.pl └── summary.pl └── setup └── env_setup.sh /LICENSE: -------------------------------------------------------------------------------- 1 | GNU AFFERO GENERAL PUBLIC LICENSE 2 | Version 3, 19 November 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU Affero General Public License is a free, copyleft license for 11 | software and other kinds of works, specifically designed to ensure 12 | cooperation with the community in the case of network server software. 13 | 14 | The licenses for most software and other practical works are designed 15 | to take away your freedom to share and change the works. By contrast, 16 | our General Public Licenses are intended to guarantee your freedom to 17 | share and change all versions of a program--to make sure it remains free 18 | software for all its users. 19 | 20 | When we speak of free software, we are referring to freedom, not 21 | price. Our General Public Licenses are designed to make sure that you 22 | have the freedom to distribute copies of free software (and charge for 23 | them if you wish), that you receive source code or can get it if you 24 | want it, that you can change the software or use pieces of it in new 25 | free programs, and that you know you can do these things. 26 | 27 | Developers that use our General Public Licenses protect your rights 28 | with two steps: (1) assert copyright on the software, and (2) offer 29 | you this License which gives you legal permission to copy, distribute 30 | and/or modify the software. 31 | 32 | A secondary benefit of defending all users' freedom is that 33 | improvements made in alternate versions of the program, if they 34 | receive widespread use, become available for other developers to 35 | incorporate. Many developers of free software are heartened and 36 | encouraged by the resulting cooperation. However, in the case of 37 | software used on network servers, this result may fail to come about. 38 | The GNU General Public License permits making a modified version and 39 | letting the public access it on a server without ever releasing its 40 | source code to the public. 41 | 42 | The GNU Affero General Public License is designed specifically to 43 | ensure that, in such cases, the modified source code becomes available 44 | to the community. It requires the operator of a network server to 45 | provide the source code of the modified version running there to the 46 | users of that server. Therefore, public use of a modified version, on 47 | a publicly accessible server, gives the public access to the source 48 | code of the modified version. 49 | 50 | An older license, called the Affero General Public License and 51 | published by Affero, was designed to accomplish similar goals. This is 52 | a different license, not a version of the Affero GPL, but Affero has 53 | released a new version of the Affero GPL which permits relicensing under 54 | this license. 55 | 56 | The precise terms and conditions for copying, distribution and 57 | modification follow. 58 | 59 | TERMS AND CONDITIONS 60 | 61 | 0. Definitions. 62 | 63 | "This License" refers to version 3 of the GNU Affero General Public License. 64 | 65 | "Copyright" also means copyright-like laws that apply to other kinds of 66 | works, such as semiconductor masks. 67 | 68 | "The Program" refers to any copyrightable work licensed under this 69 | License. Each licensee is addressed as "you". "Licensees" and 70 | "recipients" may be individuals or organizations. 71 | 72 | To "modify" a work means to copy from or adapt all or part of the work 73 | in a fashion requiring copyright permission, other than the making of an 74 | exact copy. The resulting work is called a "modified version" of the 75 | earlier work or a work "based on" the earlier work. 76 | 77 | A "covered work" means either the unmodified Program or a work based 78 | on the Program. 79 | 80 | To "propagate" a work means to do anything with it that, without 81 | permission, would make you directly or secondarily liable for 82 | infringement under applicable copyright law, except executing it on a 83 | computer or modifying a private copy. Propagation includes copying, 84 | distribution (with or without modification), making available to the 85 | public, and in some countries other activities as well. 86 | 87 | To "convey" a work means any kind of propagation that enables other 88 | parties to make or receive copies. Mere interaction with a user through 89 | a computer network, with no transfer of a copy, is not conveying. 90 | 91 | An interactive user interface displays "Appropriate Legal Notices" 92 | to the extent that it includes a convenient and prominently visible 93 | feature that (1) displays an appropriate copyright notice, and (2) 94 | tells the user that there is no warranty for the work (except to the 95 | extent that warranties are provided), that licensees may convey the 96 | work under this License, and how to view a copy of this License. If 97 | the interface presents a list of user commands or options, such as a 98 | menu, a prominent item in the list meets this criterion. 99 | 100 | 1. Source Code. 101 | 102 | The "source code" for a work means the preferred form of the work 103 | for making modifications to it. "Object code" means any non-source 104 | form of a work. 105 | 106 | A "Standard Interface" means an interface that either is an official 107 | standard defined by a recognized standards body, or, in the case of 108 | interfaces specified for a particular programming language, one that 109 | is widely used among developers working in that language. 110 | 111 | The "System Libraries" of an executable work include anything, other 112 | than the work as a whole, that (a) is included in the normal form of 113 | packaging a Major Component, but which is not part of that Major 114 | Component, and (b) serves only to enable use of the work with that 115 | Major Component, or to implement a Standard Interface for which an 116 | implementation is available to the public in source code form. A 117 | "Major Component", in this context, means a major essential component 118 | (kernel, window system, and so on) of the specific operating system 119 | (if any) on which the executable work runs, or a compiler used to 120 | produce the work, or an object code interpreter used to run it. 121 | 122 | The "Corresponding Source" for a work in object code form means all 123 | the source code needed to generate, install, and (for an executable 124 | work) run the object code and to modify the work, including scripts to 125 | control those activities. However, it does not include the work's 126 | System Libraries, or general-purpose tools or generally available free 127 | programs which are used unmodified in performing those activities but 128 | which are not part of the work. For example, Corresponding Source 129 | includes interface definition files associated with source files for 130 | the work, and the source code for shared libraries and dynamically 131 | linked subprograms that the work is specifically designed to require, 132 | such as by intimate data communication or control flow between those 133 | subprograms and other parts of the work. 134 | 135 | The Corresponding Source need not include anything that users 136 | can regenerate automatically from other parts of the Corresponding 137 | Source. 138 | 139 | The Corresponding Source for a work in source code form is that 140 | same work. 141 | 142 | 2. Basic Permissions. 143 | 144 | All rights granted under this License are granted for the term of 145 | copyright on the Program, and are irrevocable provided the stated 146 | conditions are met. This License explicitly affirms your unlimited 147 | permission to run the unmodified Program. The output from running a 148 | covered work is covered by this License only if the output, given its 149 | content, constitutes a covered work. This License acknowledges your 150 | rights of fair use or other equivalent, as provided by copyright law. 151 | 152 | You may make, run and propagate covered works that you do not 153 | convey, without conditions so long as your license otherwise remains 154 | in force. You may convey covered works to others for the sole purpose 155 | of having them make modifications exclusively for you, or provide you 156 | with facilities for running those works, provided that you comply with 157 | the terms of this License in conveying all material for which you do 158 | not control copyright. Those thus making or running the covered works 159 | for you must do so exclusively on your behalf, under your direction 160 | and control, on terms that prohibit them from making any copies of 161 | your copyrighted material outside their relationship with you. 162 | 163 | Conveying under any other circumstances is permitted solely under 164 | the conditions stated below. Sublicensing is not allowed; section 10 165 | makes it unnecessary. 166 | 167 | 3. Protecting Users' Legal Rights From Anti-Circumvention Law. 168 | 169 | No covered work shall be deemed part of an effective technological 170 | measure under any applicable law fulfilling obligations under article 171 | 11 of the WIPO copyright treaty adopted on 20 December 1996, or 172 | similar laws prohibiting or restricting circumvention of such 173 | measures. 174 | 175 | When you convey a covered work, you waive any legal power to forbid 176 | circumvention of technological measures to the extent such circumvention 177 | is effected by exercising rights under this License with respect to 178 | the covered work, and you disclaim any intention to limit operation or 179 | modification of the work as a means of enforcing, against the work's 180 | users, your or third parties' legal rights to forbid circumvention of 181 | technological measures. 182 | 183 | 4. Conveying Verbatim Copies. 184 | 185 | You may convey verbatim copies of the Program's source code as you 186 | receive it, in any medium, provided that you conspicuously and 187 | appropriately publish on each copy an appropriate copyright notice; 188 | keep intact all notices stating that this License and any 189 | non-permissive terms added in accord with section 7 apply to the code; 190 | keep intact all notices of the absence of any warranty; and give all 191 | recipients a copy of this License along with the Program. 192 | 193 | You may charge any price or no price for each copy that you convey, 194 | and you may offer support or warranty protection for a fee. 195 | 196 | 5. Conveying Modified Source Versions. 197 | 198 | You may convey a work based on the Program, or the modifications to 199 | produce it from the Program, in the form of source code under the 200 | terms of section 4, provided that you also meet all of these conditions: 201 | 202 | a) The work must carry prominent notices stating that you modified 203 | it, and giving a relevant date. 204 | 205 | b) The work must carry prominent notices stating that it is 206 | released under this License and any conditions added under section 207 | 7. This requirement modifies the requirement in section 4 to 208 | "keep intact all notices". 209 | 210 | c) You must license the entire work, as a whole, under this 211 | License to anyone who comes into possession of a copy. This 212 | License will therefore apply, along with any applicable section 7 213 | additional terms, to the whole of the work, and all its parts, 214 | regardless of how they are packaged. This License gives no 215 | permission to license the work in any other way, but it does not 216 | invalidate such permission if you have separately received it. 217 | 218 | d) If the work has interactive user interfaces, each must display 219 | Appropriate Legal Notices; however, if the Program has interactive 220 | interfaces that do not display Appropriate Legal Notices, your 221 | work need not make them do so. 222 | 223 | A compilation of a covered work with other separate and independent 224 | works, which are not by their nature extensions of the covered work, 225 | and which are not combined with it such as to form a larger program, 226 | in or on a volume of a storage or distribution medium, is called an 227 | "aggregate" if the compilation and its resulting copyright are not 228 | used to limit the access or legal rights of the compilation's users 229 | beyond what the individual works permit. Inclusion of a covered work 230 | in an aggregate does not cause this License to apply to the other 231 | parts of the aggregate. 232 | 233 | 6. Conveying Non-Source Forms. 234 | 235 | You may convey a covered work in object code form under the terms 236 | of sections 4 and 5, provided that you also convey the 237 | machine-readable Corresponding Source under the terms of this License, 238 | in one of these ways: 239 | 240 | a) Convey the object code in, or embodied in, a physical product 241 | (including a physical distribution medium), accompanied by the 242 | Corresponding Source fixed on a durable physical medium 243 | customarily used for software interchange. 244 | 245 | b) Convey the object code in, or embodied in, a physical product 246 | (including a physical distribution medium), accompanied by a 247 | written offer, valid for at least three years and valid for as 248 | long as you offer spare parts or customer support for that product 249 | model, to give anyone who possesses the object code either (1) a 250 | copy of the Corresponding Source for all the software in the 251 | product that is covered by this License, on a durable physical 252 | medium customarily used for software interchange, for a price no 253 | more than your reasonable cost of physically performing this 254 | conveying of source, or (2) access to copy the 255 | Corresponding Source from a network server at no charge. 256 | 257 | c) Convey individual copies of the object code with a copy of the 258 | written offer to provide the Corresponding Source. This 259 | alternative is allowed only occasionally and noncommercially, and 260 | only if you received the object code with such an offer, in accord 261 | with subsection 6b. 262 | 263 | d) Convey the object code by offering access from a designated 264 | place (gratis or for a charge), and offer equivalent access to the 265 | Corresponding Source in the same way through the same place at no 266 | further charge. You need not require recipients to copy the 267 | Corresponding Source along with the object code. If the place to 268 | copy the object code is a network server, the Corresponding Source 269 | may be on a different server (operated by you or a third party) 270 | that supports equivalent copying facilities, provided you maintain 271 | clear directions next to the object code saying where to find the 272 | Corresponding Source. Regardless of what server hosts the 273 | Corresponding Source, you remain obligated to ensure that it is 274 | available for as long as needed to satisfy these requirements. 275 | 276 | e) Convey the object code using peer-to-peer transmission, provided 277 | you inform other peers where the object code and Corresponding 278 | Source of the work are being offered to the general public at no 279 | charge under subsection 6d. 280 | 281 | A separable portion of the object code, whose source code is excluded 282 | from the Corresponding Source as a System Library, need not be 283 | included in conveying the object code work. 284 | 285 | A "User Product" is either (1) a "consumer product", which means any 286 | tangible personal property which is normally used for personal, family, 287 | or household purposes, or (2) anything designed or sold for incorporation 288 | into a dwelling. In determining whether a product is a consumer product, 289 | doubtful cases shall be resolved in favor of coverage. For a particular 290 | product received by a particular user, "normally used" refers to a 291 | typical or common use of that class of product, regardless of the status 292 | of the particular user or of the way in which the particular user 293 | actually uses, or expects or is expected to use, the product. A product 294 | is a consumer product regardless of whether the product has substantial 295 | commercial, industrial or non-consumer uses, unless such uses represent 296 | the only significant mode of use of the product. 297 | 298 | "Installation Information" for a User Product means any methods, 299 | procedures, authorization keys, or other information required to install 300 | and execute modified versions of a covered work in that User Product from 301 | a modified version of its Corresponding Source. The information must 302 | suffice to ensure that the continued functioning of the modified object 303 | code is in no case prevented or interfered with solely because 304 | modification has been made. 305 | 306 | If you convey an object code work under this section in, or with, or 307 | specifically for use in, a User Product, and the conveying occurs as 308 | part of a transaction in which the right of possession and use of the 309 | User Product is transferred to the recipient in perpetuity or for a 310 | fixed term (regardless of how the transaction is characterized), the 311 | Corresponding Source conveyed under this section must be accompanied 312 | by the Installation Information. But this requirement does not apply 313 | if neither you nor any third party retains the ability to install 314 | modified object code on the User Product (for example, the work has 315 | been installed in ROM). 316 | 317 | The requirement to provide Installation Information does not include a 318 | requirement to continue to provide support service, warranty, or updates 319 | for a work that has been modified or installed by the recipient, or for 320 | the User Product in which it has been modified or installed. Access to a 321 | network may be denied when the modification itself materially and 322 | adversely affects the operation of the network or violates the rules and 323 | protocols for communication across the network. 324 | 325 | Corresponding Source conveyed, and Installation Information provided, 326 | in accord with this section must be in a format that is publicly 327 | documented (and with an implementation available to the public in 328 | source code form), and must require no special password or key for 329 | unpacking, reading or copying. 330 | 331 | 7. Additional Terms. 332 | 333 | "Additional permissions" are terms that supplement the terms of this 334 | License by making exceptions from one or more of its conditions. 335 | Additional permissions that are applicable to the entire Program shall 336 | be treated as though they were included in this License, to the extent 337 | that they are valid under applicable law. If additional permissions 338 | apply only to part of the Program, that part may be used separately 339 | under those permissions, but the entire Program remains governed by 340 | this License without regard to the additional permissions. 341 | 342 | When you convey a copy of a covered work, you may at your option 343 | remove any additional permissions from that copy, or from any part of 344 | it. (Additional permissions may be written to require their own 345 | removal in certain cases when you modify the work.) You may place 346 | additional permissions on material, added by you to a covered work, 347 | for which you have or can give appropriate copyright permission. 348 | 349 | Notwithstanding any other provision of this License, for material you 350 | add to a covered work, you may (if authorized by the copyright holders of 351 | that material) supplement the terms of this License with terms: 352 | 353 | a) Disclaiming warranty or limiting liability differently from the 354 | terms of sections 15 and 16 of this License; or 355 | 356 | b) Requiring preservation of specified reasonable legal notices or 357 | author attributions in that material or in the Appropriate Legal 358 | Notices displayed by works containing it; or 359 | 360 | c) Prohibiting misrepresentation of the origin of that material, or 361 | requiring that modified versions of such material be marked in 362 | reasonable ways as different from the original version; or 363 | 364 | d) Limiting the use for publicity purposes of names of licensors or 365 | authors of the material; or 366 | 367 | e) Declining to grant rights under trademark law for use of some 368 | trade names, trademarks, or service marks; or 369 | 370 | f) Requiring indemnification of licensors and authors of that 371 | material by anyone who conveys the material (or modified versions of 372 | it) with contractual assumptions of liability to the recipient, for 373 | any liability that these contractual assumptions directly impose on 374 | those licensors and authors. 375 | 376 | All other non-permissive additional terms are considered "further 377 | restrictions" within the meaning of section 10. If the Program as you 378 | received it, or any part of it, contains a notice stating that it is 379 | governed by this License along with a term that is a further 380 | restriction, you may remove that term. If a license document contains 381 | a further restriction but permits relicensing or conveying under this 382 | License, you may add to a covered work material governed by the terms 383 | of that license document, provided that the further restriction does 384 | not survive such relicensing or conveying. 385 | 386 | If you add terms to a covered work in accord with this section, you 387 | must place, in the relevant source files, a statement of the 388 | additional terms that apply to those files, or a notice indicating 389 | where to find the applicable terms. 390 | 391 | Additional terms, permissive or non-permissive, may be stated in the 392 | form of a separately written license, or stated as exceptions; 393 | the above requirements apply either way. 394 | 395 | 8. Termination. 396 | 397 | You may not propagate or modify a covered work except as expressly 398 | provided under this License. Any attempt otherwise to propagate or 399 | modify it is void, and will automatically terminate your rights under 400 | this License (including any patent licenses granted under the third 401 | paragraph of section 11). 402 | 403 | However, if you cease all violation of this License, then your 404 | license from a particular copyright holder is reinstated (a) 405 | provisionally, unless and until the copyright holder explicitly and 406 | finally terminates your license, and (b) permanently, if the copyright 407 | holder fails to notify you of the violation by some reasonable means 408 | prior to 60 days after the cessation. 409 | 410 | Moreover, your license from a particular copyright holder is 411 | reinstated permanently if the copyright holder notifies you of the 412 | violation by some reasonable means, this is the first time you have 413 | received notice of violation of this License (for any work) from that 414 | copyright holder, and you cure the violation prior to 30 days after 415 | your receipt of the notice. 416 | 417 | Termination of your rights under this section does not terminate the 418 | licenses of parties who have received copies or rights from you under 419 | this License. If your rights have been terminated and not permanently 420 | reinstated, you do not qualify to receive new licenses for the same 421 | material under section 10. 422 | 423 | 9. Acceptance Not Required for Having Copies. 424 | 425 | You are not required to accept this License in order to receive or 426 | run a copy of the Program. Ancillary propagation of a covered work 427 | occurring solely as a consequence of using peer-to-peer transmission 428 | to receive a copy likewise does not require acceptance. However, 429 | nothing other than this License grants you permission to propagate or 430 | modify any covered work. These actions infringe copyright if you do 431 | not accept this License. Therefore, by modifying or propagating a 432 | covered work, you indicate your acceptance of this License to do so. 433 | 434 | 10. Automatic Licensing of Downstream Recipients. 435 | 436 | Each time you convey a covered work, the recipient automatically 437 | receives a license from the original licensors, to run, modify and 438 | propagate that work, subject to this License. You are not responsible 439 | for enforcing compliance by third parties with this License. 440 | 441 | An "entity transaction" is a transaction transferring control of an 442 | organization, or substantially all assets of one, or subdividing an 443 | organization, or merging organizations. If propagation of a covered 444 | work results from an entity transaction, each party to that 445 | transaction who receives a copy of the work also receives whatever 446 | licenses to the work the party's predecessor in interest had or could 447 | give under the previous paragraph, plus a right to possession of the 448 | Corresponding Source of the work from the predecessor in interest, if 449 | the predecessor has it or can get it with reasonable efforts. 450 | 451 | You may not impose any further restrictions on the exercise of the 452 | rights granted or affirmed under this License. For example, you may 453 | not impose a license fee, royalty, or other charge for exercise of 454 | rights granted under this License, and you may not initiate litigation 455 | (including a cross-claim or counterclaim in a lawsuit) alleging that 456 | any patent claim is infringed by making, using, selling, offering for 457 | sale, or importing the Program or any portion of it. 458 | 459 | 11. Patents. 460 | 461 | A "contributor" is a copyright holder who authorizes use under this 462 | License of the Program or a work on which the Program is based. The 463 | work thus licensed is called the contributor's "contributor version". 464 | 465 | A contributor's "essential patent claims" are all patent claims 466 | owned or controlled by the contributor, whether already acquired or 467 | hereafter acquired, that would be infringed by some manner, permitted 468 | by this License, of making, using, or selling its contributor version, 469 | but do not include claims that would be infringed only as a 470 | consequence of further modification of the contributor version. For 471 | purposes of this definition, "control" includes the right to grant 472 | patent sublicenses in a manner consistent with the requirements of 473 | this License. 474 | 475 | Each contributor grants you a non-exclusive, worldwide, royalty-free 476 | patent license under the contributor's essential patent claims, to 477 | make, use, sell, offer for sale, import and otherwise run, modify and 478 | propagate the contents of its contributor version. 479 | 480 | In the following three paragraphs, a "patent license" is any express 481 | agreement or commitment, however denominated, not to enforce a patent 482 | (such as an express permission to practice a patent or covenant not to 483 | sue for patent infringement). To "grant" such a patent license to a 484 | party means to make such an agreement or commitment not to enforce a 485 | patent against the party. 486 | 487 | If you convey a covered work, knowingly relying on a patent license, 488 | and the Corresponding Source of the work is not available for anyone 489 | to copy, free of charge and under the terms of this License, through a 490 | publicly available network server or other readily accessible means, 491 | then you must either (1) cause the Corresponding Source to be so 492 | available, or (2) arrange to deprive yourself of the benefit of the 493 | patent license for this particular work, or (3) arrange, in a manner 494 | consistent with the requirements of this License, to extend the patent 495 | license to downstream recipients. "Knowingly relying" means you have 496 | actual knowledge that, but for the patent license, your conveying the 497 | covered work in a country, or your recipient's use of the covered work 498 | in a country, would infringe one or more identifiable patents in that 499 | country that you have reason to believe are valid. 500 | 501 | If, pursuant to or in connection with a single transaction or 502 | arrangement, you convey, or propagate by procuring conveyance of, a 503 | covered work, and grant a patent license to some of the parties 504 | receiving the covered work authorizing them to use, propagate, modify 505 | or convey a specific copy of the covered work, then the patent license 506 | you grant is automatically extended to all recipients of the covered 507 | work and works based on it. 508 | 509 | A patent license is "discriminatory" if it does not include within 510 | the scope of its coverage, prohibits the exercise of, or is 511 | conditioned on the non-exercise of one or more of the rights that are 512 | specifically granted under this License. You may not convey a covered 513 | work if you are a party to an arrangement with a third party that is 514 | in the business of distributing software, under which you make payment 515 | to the third party based on the extent of your activity of conveying 516 | the work, and under which the third party grants, to any of the 517 | parties who would receive the covered work from you, a discriminatory 518 | patent license (a) in connection with copies of the covered work 519 | conveyed by you (or copies made from those copies), or (b) primarily 520 | for and in connection with specific products or compilations that 521 | contain the covered work, unless you entered into that arrangement, 522 | or that patent license was granted, prior to 28 March 2007. 523 | 524 | Nothing in this License shall be construed as excluding or limiting 525 | any implied license or other defenses to infringement that may 526 | otherwise be available to you under applicable patent law. 527 | 528 | 12. No Surrender of Others' Freedom. 529 | 530 | If conditions are imposed on you (whether by court order, agreement or 531 | otherwise) that contradict the conditions of this License, they do not 532 | excuse you from the conditions of this License. If you cannot convey a 533 | covered work so as to satisfy simultaneously your obligations under this 534 | License and any other pertinent obligations, then as a consequence you may 535 | not convey it at all. For example, if you agree to terms that obligate you 536 | to collect a royalty for further conveying from those to whom you convey 537 | the Program, the only way you could satisfy both those terms and this 538 | License would be to refrain entirely from conveying the Program. 539 | 540 | 13. Remote Network Interaction; Use with the GNU General Public License. 541 | 542 | Notwithstanding any other provision of this License, if you modify the 543 | Program, your modified version must prominently offer all users 544 | interacting with it remotely through a computer network (if your version 545 | supports such interaction) an opportunity to receive the Corresponding 546 | Source of your version by providing access to the Corresponding Source 547 | from a network server at no charge, through some standard or customary 548 | means of facilitating copying of software. This Corresponding Source 549 | shall include the Corresponding Source for any work covered by version 3 550 | of the GNU General Public License that is incorporated pursuant to the 551 | following paragraph. 552 | 553 | Notwithstanding any other provision of this License, you have 554 | permission to link or combine any covered work with a work licensed 555 | under version 3 of the GNU General Public License into a single 556 | combined work, and to convey the resulting work. The terms of this 557 | License will continue to apply to the part which is the covered work, 558 | but the work with which it is combined will remain governed by version 559 | 3 of the GNU General Public License. 560 | 561 | 14. Revised Versions of this License. 562 | 563 | The Free Software Foundation may publish revised and/or new versions of 564 | the GNU Affero General Public License from time to time. Such new versions 565 | will be similar in spirit to the present version, but may differ in detail to 566 | address new problems or concerns. 567 | 568 | Each version is given a distinguishing version number. If the 569 | Program specifies that a certain numbered version of the GNU Affero General 570 | Public License "or any later version" applies to it, you have the 571 | option of following the terms and conditions either of that numbered 572 | version or of any later version published by the Free Software 573 | Foundation. If the Program does not specify a version number of the 574 | GNU Affero General Public License, you may choose any version ever published 575 | by the Free Software Foundation. 576 | 577 | If the Program specifies that a proxy can decide which future 578 | versions of the GNU Affero General Public License can be used, that proxy's 579 | public statement of acceptance of a version permanently authorizes you 580 | to choose that version for the Program. 581 | 582 | Later license versions may give you additional or different 583 | permissions. However, no additional obligations are imposed on any 584 | author or copyright holder as a result of your choosing to follow a 585 | later version. 586 | 587 | 15. Disclaimer of Warranty. 588 | 589 | THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY 590 | APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT 591 | HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY 592 | OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, 593 | THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR 594 | PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM 595 | IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF 596 | ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 597 | 598 | 16. Limitation of Liability. 599 | 600 | IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING 601 | WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS 602 | THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY 603 | GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE 604 | USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF 605 | DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD 606 | PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), 607 | EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF 608 | SUCH DAMAGES. 609 | 610 | 17. Interpretation of Sections 15 and 16. 611 | 612 | If the disclaimer of warranty and limitation of liability provided 613 | above cannot be given local legal effect according to their terms, 614 | reviewing courts shall apply local law that most closely approximates 615 | an absolute waiver of all civil liability in connection with the 616 | Program, unless a warranty or assumption of liability accompanies a 617 | copy of the Program in return for a fee. 618 | 619 | END OF TERMS AND CONDITIONS 620 | 621 | How to Apply These Terms to Your New Programs 622 | 623 | If you develop a new program, and you want it to be of the greatest 624 | possible use to the public, the best way to achieve this is to make it 625 | free software which everyone can redistribute and change under these terms. 626 | 627 | To do so, attach the following notices to the program. It is safest 628 | to attach them to the start of each source file to most effectively 629 | state the exclusion of warranty; and each file should have at least 630 | the "copyright" line and a pointer to where the full notice is found. 631 | 632 | 633 | Copyright (C) 634 | 635 | This program is free software: you can redistribute it and/or modify 636 | it under the terms of the GNU Affero General Public License as published 637 | by the Free Software Foundation, either version 3 of the License, or 638 | (at your option) any later version. 639 | 640 | This program is distributed in the hope that it will be useful, 641 | but WITHOUT ANY WARRANTY; without even the implied warranty of 642 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 643 | GNU Affero General Public License for more details. 644 | 645 | You should have received a copy of the GNU Affero General Public License 646 | along with this program. If not, see . 647 | 648 | Also add information on how to contact you by electronic and paper mail. 649 | 650 | If your software can interact with users remotely through a computer 651 | network, you should also make sure that it provides a way for users to 652 | get its source. For example, if your program is a web application, its 653 | interface could display a "Source" link that leads users to an archive 654 | of the code. There are many ways you could offer source, and different 655 | solutions will be better for different programs; see section 13 for the 656 | specific requirements. 657 | 658 | You should also get your employer (if you work as a programmer) or school, 659 | if any, to sign a "copyright disclaimer" for the program, if necessary. 660 | For more information on this, and how to apply and follow the GNU AGPL, see 661 | . 662 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Polar Star 2 | 3 | This code analyzes the read depth along long-read contigs and finds outliers. 4 | 5 | ## Dependencies 6 | 7 | 8 | 9 | The Polar Star pipeline installs several common bioinformatics tools: 10 | 1. Htslib 11 | 2. Samtools 12 | 3. Bedtools 13 | 4. Vcflib 14 | 5. Minimap2 15 | 16 | These codebases have serval system library dependencies. There is a shell script that installs the dependencies (for Amazon EC2 instance). If you’re not using Amazon EC2 the setup script should help you figure out which libraries you need. 17 | 18 | ### Polar Star installs specific commits of code so that the pipeline won’t be broken as command line tools change. 19 | 20 | The pipeline is run by snakemake: http://snakemake.readthedocs.io/en/stable/ 21 | 22 | ## Setup 23 | 24 | edit the config.json file. 25 | 26 | ``` 27 | { 28 | "threads" : "4", #the number of threads available 29 | "opts" : "-x map-pb -a", #minimap2 options (advanced) 30 | "name" : "sample_name", #output prefix 31 | "lib" : "la", #a library name for the bam (most can ignore) 32 | "low_depth" : "2", #low depth cutoff 33 | "times_mean" : "3", #high depth cutoff = mean * (times_mean) 34 | "fasta_name" : "PGA1_jelly_arrow_pilon_pallidicuale.gapsplit.fasta", #full fasta name 35 | "fastq_names" : "m54120_170710_225913.subreads.fasta,m54120_170711_085749.subreads.fasta,m54120_170711_190715.subreads.fasta" #comma separated list of long-reads to align 36 | } 37 | 38 | ``` 39 | 40 | ## Running 41 | 42 | ``` 43 | snakemake -p -s Snakefile 44 | ``` 45 | 46 | ## What is Polar Star doing? 47 | 48 | 1. Aligning the long-reads to the assembly. 49 | 2. Caculating read depth at every base. 50 | 3. Smoothing the read depht in a 100bp sliding window. 51 | 4. Merging regions of high (_hd), low (_ld), and normal read depth (_nd). 52 | 5. Creating a new fasta that is broken. 53 | 6. Generates simple statistics. 54 | 55 | 56 | ## FAQ 57 | 58 | Q: What if i don't want to break on low read depth? 59 | 60 | + *A: set "low_depth" value to -1.* 61 | 62 | Q: How is the high depth caculated? 63 | 64 | + *A: Polar Star calculates the mean, then multiplies the value in "times_mean".* 65 | 66 | Q: How did you come up with the "times_mean" default? 67 | 68 | + *A: Read depth can be modeled with a negative binomial distribution, but I was too lazy. I'm using a poisson. So the mean = the standard deviation.* 69 | 70 | Q: How can I reject breaks. 71 | 72 | + *A: Edit the bed file that is the input for the "getFasta" rule.* 73 | 74 | Q: How can I add breaks. 75 | 76 | + *A: Edit the bed file that is the input for the "getFasta" rule.* 77 | 78 | Q: I already have an alignment, how can i use that? 79 | 80 | + *A: Snakemake is smart. Check the input to the "meanDepth" rule and match the file name. You'll need to change the config.json so the names match.* 81 | -------------------------------------------------------------------------------- /Snakefile: -------------------------------------------------------------------------------- 1 | 2 | configfile: "config.json" 3 | 4 | RG = "'@RG\\tID:" + config['lib'] + "\\tSM:" + config['name'] + "'" 5 | print("Read Group:", RG) 6 | 7 | FASTQ = config["fastq_names"].split(",") 8 | print("Fastqs:", FASTQ) 9 | 10 | ALN_CMD = "minimap2/minimap2 " + config['opts'] + " -t " + config['threads'] 11 | 12 | AUX_THREADS = int(config['threads']) - 1 13 | 14 | SAMPLES=config['name'] 15 | 16 | ruleorder: sortBam > makeBam 17 | 18 | rule wrappingUp : 19 | input : RESULT=expand("{sample}.new_fasta.fasta", sample=SAMPLES), BED=expand("{sample}.broken.sorted.bed", sample=SAMPLES) 20 | message: "[INFO] getting fasta" 21 | output : "RESULTS.tar.gz" 22 | shell : """ 23 | cat {input.BED} | perl scripts/summary.pl > REPORT.txt 2> MATLOCK_EXCLUDE_LIST.txt 24 | 25 | cp config.json config.json.bk 26 | 27 | tar -cvf RESULTS.tar.gz REPORT.txt MATLOCK_EXCLUDE_LIST.txt {input.RESULT} {input.BED} docs/README.md config.json.bk 28 | """ 29 | 30 | rule getFasta: 31 | message: "[INFO] getting fasta" 32 | input : BF="{sample}.broken.bed", BT="bedtools2/bin/bedtools", FA=config["fasta_name"], ST="samtools/samtools" 33 | output : RFA="{sample}.new_fasta.fasta", BD="{sample}.broken.sorted.bed" 34 | shell : """ 35 | sort -k1,1 -k2,2n {input.BF} > {output.BD} 36 | {input.BT} getfasta -name -fi {input.FA} -fo {output.RFA} -bed {output.BD} 37 | {input.ST} faidx {output.RFA} 38 | 39 | 40 | """ 41 | 42 | 43 | 44 | rule lowdepth: 45 | message: "[INFO] finding low depth regions: <= %s" % config['low_depth'] 46 | input : MEAN="{sample}.read.depth.smooth.mean.txt", SMOOTHED="{sample}.read.depth.smooth.txt", BT="bedtools2/bin/bedtools" 47 | output : "{sample}.broken.bed" 48 | params : LOW=config['low_depth'], MULT=config['times_mean'] 49 | shell : """ 50 | cat {input.SMOOTHED} | perl -lane 'print if $F[4] <= {params.LOW}' | {input.BT} merge -c 5 -o collapse -i - | perl -lane '$F[3] = "$F[0]_ld:$F[1]-$F[2]"; print join "\\t", @F' > {output} 51 | 52 | export HIGH=$(cat {input.MEAN}) 53 | echo $HIGH 54 | 55 | cat {input.SMOOTHED} | perl -lane 'print if $F[4] >= {params.MULT} * '"$HIGH"';' | {input.BT} merge -c 5 -o collapse -i - | perl -lane '$F[3] = "$F[0]_hd:$F[1]-$F[2]"; print join "\\t", @F' >> {output} 56 | 57 | cat {input.SMOOTHED} | perl -lane 'print if ($F[4] < {params.MULT} * '"$HIGH"' ) && ($F[4] > {params.LOW})' | {input.BT} merge -c 5 -o collapse -i - | perl -lane '$F[3] = "$F[0]_nd:$F[1]-$F[2]"; print join "\\t", @F' >> {output} 58 | 59 | """ 60 | 61 | rule meanSmooth: 62 | message : "[INFO] calculating mean depth" 63 | input : "{sample}.read.depth.smooth.txt" 64 | output : "{sample}.read.depth.smooth.mean.txt" 65 | shell : """ 66 | cat {input} | perl scripts/mean.pl > {output} 67 | """ 68 | 69 | rule smoother: 70 | message : "[INFO] smoothing read depth" 71 | input : DEPTH="{sample}.read.depth.txt", SMOOTHER="vcflib/bin/smoother" 72 | output : "{sample}.read.depth.smooth.txt" 73 | shell : """ 74 | {input.SMOOTHER} -o col3 -w 100 -s 100 -t -f {input.DEPTH} > {output} 75 | """ 76 | 77 | 78 | rule meanDepth: 79 | message: "[INFO] getting read depth." 80 | input : SORTED_BAM="{sample}.sort.bam", ST="samtools/samtools" 81 | output : "{sample}.read.depth.txt" 82 | shell : """ 83 | {input.ST} depth -aa {input.SORTED_BAM} > {output} 84 | """ 85 | 86 | rule sortBam: 87 | message: "[INFO] sorting BAM." 88 | input : BAM="{sample}.bam", ST="samtools/samtools" 89 | output : protected("{sample}.sort.bam") 90 | shell : """ 91 | {input.ST} sort -@ {AUX_THREADS} {input.BAM} -o {output} 92 | """ 93 | 94 | rule makeBam: 95 | message: "[INFO] converting sam to bam." 96 | input : SAM="{sample}.sam", ST="samtools/samtools" 97 | output : temp("{sample}.bam") 98 | shell : """ 99 | {input.ST} view -bS -@ {AUX_THREADS} {input.SAM} > {output} 100 | """ 101 | 102 | rule makeSam: 103 | message: "[INFO] running alignment." 104 | input : FA=config["fasta_name"], MM="minimap2/minimap2", FQ=FASTQ 105 | output : temp("{sample}.sam") 106 | shell : """ 107 | {ALN_CMD} {input.FA} {input.FQ} > {output} 108 | """ 109 | 110 | rule samtools: 111 | message: "[INFO] installing samtools." 112 | input : "htslib/libhts.a" 113 | output : "samtools/samtools" 114 | shell : """ 115 | git clone https://github.com/samtools/samtools.git 116 | cd samtools 117 | git checkout 6d79411685d8f0fbb34e123f52d72b63271f4dcb 118 | autoheader 119 | autoconf -Wno-syntax 120 | ./configure 121 | make 122 | """ 123 | 124 | rule htslib: 125 | message: "[INFO] installing htslib" 126 | output: "htslib/libhts.a" 127 | shell: """ 128 | git clone https://github.com/samtools/htslib.git 129 | cd htslib 130 | git checkout 209f94ba28d62a566c77e3fbf034e3ee76807815 131 | autoheader 132 | autoconf 133 | ./configure 134 | make 135 | """ 136 | 137 | 138 | rule vcflib: 139 | message: "[INFO] installing vcflib" 140 | output : "vcflib/bin/smoother" 141 | shell : """ 142 | rm -rf vcflib 143 | git clone --recursive https://github.com/vcflib/vcflib.git 144 | cd vcflib 145 | git checkout b17eed65ed6b40f1244c4f09ae86800e9ae9a1d6 146 | make 147 | """ 148 | 149 | 150 | rule gdrive : 151 | message: "[INFO] installing gdrive." 152 | output : "/home/ec2-user/go/bin/gdrive" 153 | shell : """ 154 | go get github.com/prasmussen/gdrive 155 | """ 156 | 157 | 158 | rule minimap2: 159 | message: "[INFO] installing minimap2." 160 | output : "minimap2/minimap2" 161 | shell : """ 162 | git clone https://github.com/lh3/minimap2.git 163 | cd minimap2 164 | git checkout 39a96662463c3f0dd8c64c70445fc0261721f010 165 | make 166 | """ 167 | 168 | rule bedtools2: 169 | message: "[INFO] installing bedtools2" 170 | output: "bedtools2/bin/bedtools" 171 | shell: """ 172 | rm -rf bedtools2 173 | git clone https://github.com/arq5x/bedtools2.git 174 | cd bedtools2 175 | git checkout f3bc2435d6ec41dfaff148a18034d4610439aa6a 176 | make 177 | """ 178 | -------------------------------------------------------------------------------- /config.json: -------------------------------------------------------------------------------- 1 | { 2 | "threads" : "4", 3 | "opts" : "-x map-pb -a", 4 | "name" : "sample_name", 5 | "lib" : "la", 6 | "low_depth" : "2", 7 | "times_mean" : "3", 8 | "fasta_name" : "PGA1_jelly_arrow_pilon_pallidicuale.gapsplit.fasta", 9 | "fastq_names" : "m54120_170710_225913.subreads.fasta,m54120_170711_085749.subreads.fasta,m54120_170711_190715.subreads.fasta" 10 | } 11 | -------------------------------------------------------------------------------- /docs/README.md: -------------------------------------------------------------------------------- 1 | # Polar Star Contig Breaking 2 | 3 | ## REPORT.txt 4 | 5 | This file contains the number of bases that are high normal or low. 6 | 7 | ## MATLOCK_EXCLUDE_LIST.txt 8 | 9 | The broken contigs that are high or low and should be excluded from scaffolding. 10 | 11 | ## {sample}.broken.sorted.bed 12 | 13 | The regions for the broken original fasta 14 | 15 | ## {sample}.new_fasta.fasta 16 | 17 | The new fasta broken on read depth 18 | 19 | ## config.json.bk 20 | 21 | The settings used to generate the resulting fasta 22 | 23 | -------------------------------------------------------------------------------- /scripts/mean.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | use warnings; 3 | use strict ; 4 | 5 | my $sum = 0; 6 | my $n = 0; 7 | 8 | 9 | while(){ 10 | chomp; 11 | my @l = split /\t/, $_; 12 | $sum += $l[4]; 13 | $n++; 14 | } 15 | 16 | my $mean = $sum / $n; 17 | 18 | print STDERR "sum\t$sum\n"; 19 | print STDERR "n\t$n\n"; 20 | 21 | print $mean; 22 | -------------------------------------------------------------------------------- /scripts/summary.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | use warnings; 3 | use strict ; 4 | 5 | my $low = 0; 6 | my $normal = 0; 7 | my $high = 0; 8 | my $total = 0; 9 | 10 | while(){ 11 | chomp; 12 | my @l = split /\t/, $_; 13 | my $len = $l[2] - $l[1]; 14 | $low += $len if($_ =~ /_ld/) ; 15 | $normal += $len if($_ =~ /_nd/) ; 16 | $high += $len if($_ =~ /_hd/) ; 17 | $total += $len; 18 | 19 | print STDERR "$l[3]," if($_ !~ /_nd/); 20 | 21 | } 22 | 23 | my $phi = ($high / $total) * 100; 24 | my $plo = ($low / $total) * 100; 25 | my $pno = ($normal / $total) * 100; 26 | 27 | print "#name\tpercent\tbases\n"; 28 | print "hi\t$phi\t$high\n"; 29 | print "low\t$plo\t$low\n"; 30 | print "normal\t$pno\t$normal\n"; 31 | -------------------------------------------------------------------------------- /setup/env_setup.sh: -------------------------------------------------------------------------------- 1 | sudo yum -y groupinstall "Development Tools" 2 | sudo yum -y install emacs 3 | sudo yum -y install git 4 | sudo yum -y install python36 5 | sudo yum -y install go 6 | sudo yum -y install zlib-devel 7 | sudo yum -y install ncurses-devel 8 | sudo yum -y install autoconf 9 | sudo yum -y install bzip2-devel-1.0.6-8.12.amzn1.x86_64 10 | sudo yum -y install xz-devel-5.1.2-12alpha.12.amzn1.x86_64 11 | 12 | sudo yum -y install python36-devel 13 | sudo python3.6 -m pip install --upgrade pip 14 | sudo python3.6 -m pip install --upgrade virtualenvwrapper 15 | sudo python3.6 -m pip install --upgrade snakemake 16 | 17 | 18 | virtualenv -p python36 ~/py_36_env 19 | source ~/py_36_env/bin/activate 20 | --------------------------------------------------------------------------------