test_variantkey.py

"""Tests for variantkey module."""

# test_npvk.py
# @category   Libraries
# @author     Nicola Asuni <nicola.asuni@genomicsplc.com>
# @copyright  2017-2018 GENOMICS plc
# @license    MIT (see LICENSE)
# @link       https://github.com/genomicsplc/variantkey

import pyvariantkey.variantkey as pyvk
import numpy as np
import os
from unittest import TestCase


# 0:chrom, 1:vkchrom, 2:pos, 3:vkpos, 4:vkrefalt, 5:vk, 6:vs, 7:ref, 8:alt
vtd = np.array([
    (b"chr1", 1, 268435455, 0x0fffffff, 0x08b80000, 0x0fffffff88b80000, b"0fffffff88b80000", b"C", b"T"),
    (b"CHR01", 1, 324675, 0x0004f443, 0x08c80000, 0x08027a2188c80000, b"08027a2188c80000", b"G", b"C"),
    (b"1", 1, 0, 0x00000000, 0x3c6f5d8f, 0x080000003c6f5d8f, b"080000003c6f5d8f", b"ACCTCACCAGGCCCAGCTCATGCTTCTTTGCAG", b"A"),
    (b"1", 1, 268435455, 0x0fffffff, 0x0ae2503b, 0x0fffffff8ae2503b, b"0fffffff8ae2503b", b"ACCAGGCCCAGCTCATGCTTCTTTGCAGCCTCT", b"A"),
    (b"1", 1, 324683, 0x0004f44b, 0x08b00000, 0x08027a2588b00000, b"08027a2588b00000", b"C", b"G"),
    (b"1", 1, 324692, 0x0004f454, 0x13ace339, 0x08027a2a13ace339, b"08027a2a13ace339", b"N", b"A"),
    (b"1", 1, 324695, 0x0004f457, 0x6d669117, 0x08027a2bed669117, b"08027a2bed669117", b"ATGCTTCTTTGCAGCCTCTCCAGGCCCAGCTCC", b"A"),
    (b"1", 1, 324728, 0x0004f478, 0x08e80000, 0x08027a3c08e80000, b"08027a3c08e80000", b"T", b"C"),
    (b"1", 1, 1, 0x00000001, 0x2db746f9, 0x08000000adb746f9, b"08000000adb746f9", b"TGGCCCCTCCAGGCCCAGCCTCTGCCTCCCGTC", b"T"),
    (b"1", 1, 324739, 0x0004f483, 0x66f83195, 0x08027a41e6f83195, b"08027a41e6f83195", b"ACGTUWSMKRYBDHVN", b"A*C*G*T*U*W*S*M*K*R*Y*B*D*H*V*N"),
    (b"1", 1, 324750, 0x0004f48e, 0x08d80000, 0x08027a4708d80000, b"08027a4708d80000", b"G", b"T"),
    (b"2", 2, 28001, 0x00006d61, 0x08c00000, 0x100036b088c00000, b"100036b088c00000", b"G", b"A"),
    (b"2", 2, 28003, 0x00006d63, 0x08c80000, 0x100036b188c80000, b"100036b188c80000", b"G", b"C"),
    (b"2", 2, 28005, 0x00006d65, 0x08900000, 0x100036b288900000, b"100036b288900000", b"A", b"G"),
    (b"2", 2, 28013, 0x00006d6d, 0x08e80000, 0x100036b688e80000, b"100036b688e80000", b"T", b"C"),
    (b"2", 2, 28017, 0x00006d71, 0x36c70401, 0x100036b8b6c70401, b"100036b8b6c70401", b"CAATTGTGAAGCAGTG", b"C"),
    (b"2", 2, 28045, 0x00006d8d, 0x08900000, 0x100036c688900000, b"100036c688900000", b"A", b"G"),
    (b"2", 2, 28056, 0x00006d98, 0x08900000, 0x100036cc08900000, b"100036cc08900000", b"A", b"G"),
    (b"2", 2, 28057, 0x00006d99, 0x08e80000, 0x100036cc88e80000, b"100036cc88e80000", b"T", b"C"),
    (b"2", 2, 28058, 0x00006d9a, 0x328d8b62, 0x100036cd328d8b62, b"100036cd328d8b62", b"ACGTAC", b"CGTAC"),
    (b"2", 2, 28067, 0x00006da3, 0x0d436362, 0x100036d18d436362, b"100036d18d436362", b"G", b"ACGTACGTAC"),
    (b"2", 2, 28106, 0x00006dca, 0x508d8d8c, 0x100036e5508d8d8c, b"100036e5508d8d8c", b"ACGTACGTAC", b"G"),
    (b"2", 2, 28136, 0x00006de8, 0x097c0000, 0x100036f4097c0000, b"100036f4097c0000", b"T", b"TG"),
    (b"3", 3, 74852, 0x00012464, 0x08c00000, 0x1800923208c00000, b"1800923208c00000", b"G", b"A"),
    (b"3", 3, 74859, 0x0001246b, 0x08c00000, 0x1800923588c00000, b"1800923588c00000", b"G", b"A"),
    (b"3", 3, 74915, 0x000124a3, 0x19160000, 0x1800925199160000, b"1800925199160000", b"AGT", b"AA"),
    (b"3", 3, 74915, 0x000124a3, 0x10900000, 0x1800925190900000, b"1800925190900000", b"AG", b"A"),
    (b"3", 3, 74916, 0x000124a4, 0x10dc0000, 0x1800925210dc0000, b"1800925210dc0000", b"GT", b"G"),
    (b"3", 3, 74916, 0x000124a4, 0x10dc0000, 0x1800925210dc0000, b"1800925210dc0000", b"GT", b"G"),
    (b"3", 3, 74917, 0x000124a5, 0x08e00000, 0x1800925288e00000, b"1800925288e00000", b"T", b"A"),
    (b"3", 3, 74923, 0x000124ab, 0x08c00000, 0x1800925588c00000, b"1800925588c00000", b"G", b"A"),
    (b"3", 3, 74930, 0x000124b2, 0x08b80000, 0x1800925908b80000, b"1800925908b80000", b"C", b"T"),
    (b"3", 3, 74931, 0x000124b3, 0x08980000, 0x1800925988980000, b"1800925988980000", b"A", b"T"),
    (b"3", 3, 74958, 0x000124ce, 0x08b80000, 0x1800926708b80000, b"1800926708b80000", b"C", b"T"),
    (b"3", 3, 74970, 0x000124da, 0x28b9e800, 0x1800926d28b9e800, b"1800926d28b9e800", b"CTATT", b"C"),
    (b"3", 3, 74970, 0x000124da, 0x28b9e800, 0x1800926d28b9e800, b"1800926d28b9e800", b"CTATT", b"C"),
    (b"4", 4, 60482, 0x0000ec42, 0x08e80000, 0x2000762108e80000, b"2000762108e80000", b"T", b"C"),
    (b"4", 4, 60502, 0x0000ec56, 0x09060000, 0x2000762b09060000, b"2000762b09060000", b"A", b"AT"),
    (b"4", 4, 60502, 0x0000ec56, 0x10980000, 0x2000762b10980000, b"2000762b10980000", b"AT", b"A"),
    (b"4", 4, 60502, 0x0000ec56, 0x189e0000, 0x2000762b189e0000, b"2000762b189e0000", b"ATT", b"A"),
    (b"4", 4, 60502, 0x0000ec56, 0x09060000, 0x2000762b09060000, b"2000762b09060000", b"A", b"AT"),
    (b"4", 4, 60502, 0x0000ec56, 0x09060000, 0x2000762b09060000, b"2000762b09060000", b"A", b"AT"),
    (b"4", 4, 60502, 0x0000ec56, 0x10980000, 0x2000762b10980000, b"2000762b10980000", b"AT", b"A"),
    (b"4", 4, 60513, 0x0000ec61, 0x08e00000, 0x2000763088e00000, b"2000763088e00000", b"T", b"A"),
    (b"4", 4, 60569, 0x0000ec99, 0x08c00000, 0x2000764c88c00000, b"2000764c88c00000", b"G", b"A"),
    (b"4", 4, 60622, 0x0000ecce, 0x08c00000, 0x2000766708c00000, b"2000766708c00000", b"G", b"A"),
    (b"4", 4, 60683, 0x0000ed0b, 0x08c00000, 0x2000768588c00000, b"2000768588c00000", b"G", b"A"),
    (b"4", 4, 60819, 0x0000ed93, 0x08e80000, 0x200076c988e80000, b"200076c988e80000", b"T", b"C"),
    (b"4", 4, 60835, 0x0000eda3, 0x08b80000, 0x200076d188b80000, b"200076d188b80000", b"C", b"T"),
    (b"4", 4, 60867, 0x0000edc3, 0x08b80000, 0x200076e188b80000, b"200076e188b80000", b"C", b"T"),
    (b"5", 5, 28314, 0x00006e9a, 0x10980000, 0x2800374d10980000, b"2800374d10980000", b"AT", b"A"),
    (b"5", 5, 28329, 0x00006ea9, 0x08c80000, 0x2800375488c80000, b"2800375488c80000", b"G", b"C"),
    (b"5", 5, 28338, 0x00006eb2, 0x08b80000, 0x2800375908b80000, b"2800375908b80000", b"C", b"T"),
    (b"5", 5, 28341, 0x00006eb5, 0x08b80000, 0x2800375a88b80000, b"2800375a88b80000", b"C", b"T"),
    (b"5", 5, 28342, 0x00006eb6, 0x08c00000, 0x2800375b08c00000, b"2800375b08c00000", b"G", b"A"),
    (b"5", 5, 28373, 0x00006ed5, 0x08e80000, 0x2800376a88e80000, b"2800376a88e80000", b"T", b"C"),
    (b"5", 5, 28375, 0x00006ed7, 0x08a00000, 0x2800376b88a00000, b"2800376b88a00000", b"C", b"A"),
    (b"5", 5, 28383, 0x00006edf, 0x08b80000, 0x2800376f88b80000, b"2800376f88b80000", b"C", b"T"),
    (b"5", 5, 28405, 0x00006ef5, 0x08900000, 0x2800377a88900000, b"2800377a88900000", b"A", b"G"),
    (b"5", 5, 28421, 0x00006f05, 0x08e80000, 0x2800378288e80000, b"2800378288e80000", b"T", b"C"),
    (b"5", 5, 28510, 0x00006f5e, 0x08b80000, 0x280037af08b80000, b"280037af08b80000", b"C", b"T"),
    (b"5", 5, 28518, 0x00006f66, 0x08e80000, 0x280037b308e80000, b"280037b308e80000", b"T", b"C"),
    (b"5", 5, 28528, 0x00006f70, 0x08c00000, 0x280037b808c00000, b"280037b808c00000", b"G", b"A"),
    (b"5", 5, 28552, 0x00006f88, 0x08e00000, 0x280037c408e00000, b"280037c408e00000", b"T", b"A"),
    (b"5", 5, 28572, 0x00006f9c, 0x08d80000, 0x280037ce08d80000, b"280037ce08d80000", b"G", b"T"),
    (b"6", 6, 193224, 0x0002f2c8, 0x19550000, 0x3001796419550000, b"3001796419550000", b"GGG", b"GA"),
    (b"6", 6, 193225, 0x0002f2c9, 0x08c00000, 0x3001796488c00000, b"3001796488c00000", b"G", b"A"),
    (b"6", 6, 193226, 0x0002f2ca, 0x08c00000, 0x3001796508c00000, b"3001796508c00000", b"G", b"A"),
    (b"6", 6, 193238, 0x0002f2d6, 0x08900000, 0x3001796b08900000, b"3001796b08900000", b"A", b"G"),
    (b"6", 6, 193297, 0x0002f311, 0x10ba0000, 0x3001798890ba0000, b"3001798890ba0000", b"CT", b"C"),
    (b"6", 6, 193309, 0x0002f31d, 0x08900000, 0x3001798e88900000, b"3001798e88900000", b"A", b"G"),
    (b"6", 6, 193311, 0x0002f31f, 0x08c00000, 0x3001798f88c00000, b"3001798f88c00000", b"G", b"A"),
    (b"6", 6, 193321, 0x0002f329, 0x28b76800, 0x30017994a8b76800, b"30017994a8b76800", b"CGTGT", b"C"),
    (b"6", 6, 193321, 0x0002f329, 0x28b76800, 0x30017994a8b76800, b"30017994a8b76800", b"CGTGT", b"C"),
    (b"6", 6, 193321, 0x0002f329, 0x18b68000, 0x3001799498b68000, b"3001799498b68000", b"CGT", b"C"),
    (b"6", 6, 193322, 0x0002f32a, 0x08c00000, 0x3001799508c00000, b"3001799508c00000", b"G", b"A"),
    (b"6", 6, 193329, 0x0002f331, 0x1ae9db00, 0x300179989ae9db00, b"300179989ae9db00", b"TCA", b"TGTCG"),
    (b"6", 6, 193329, 0x0002f331, 0x2269f680, 0x30017998a269f680, b"30017998a269f680", b"TCAT", b"TGTC"),
    (b"6", 6, 193331, 0x0002f333, 0x08900000, 0x3001799988900000, b"3001799988900000", b"A", b"G"),
    (b"6", 6, 193335, 0x0002f337, 0x18d90000, 0x3001799b98d90000, b"3001799b98d90000", b"GTA", b"G"),
    (b"6", 6, 193335, 0x0002f337, 0x18d90000, 0x3001799b98d90000, b"3001799b98d90000", b"GTA", b"G"),
    (b"7", 7, 2287944, 0x0022e948, 0x08b80000, 0x381174a408b80000, b"381174a408b80000", b"C", b"T"),
    (b"7", 7, 2287972, 0x0022e964, 0x08e80000, 0x381174b208e80000, b"381174b208e80000", b"T", b"C"),
    (b"7", 7, 2287999, 0x0022e97f, 0x08c00000, 0x381174bf88c00000, b"381174bf88c00000", b"G", b"A"),
    (b"7", 7, 2288016, 0x0022e990, 0x08c00000, 0x381174c808c00000, b"381174c808c00000", b"G", b"A"),
    (b"7", 7, 2288048, 0x0022e9b0, 0x08c00000, 0x381174d808c00000, b"381174d808c00000", b"G", b"A"),
    (b"7", 7, 2288064, 0x0022e9c0, 0x0a87b800, 0x381174e00a87b800, b"381174e00a87b800", b"A", b"ATTCT"),
    (b"7", 7, 2288095, 0x0022e9df, 0x08b80000, 0x381174ef88b80000, b"381174ef88b80000", b"C", b"T"),
    (b"7", 7, 2288096, 0x0022e9e0, 0x08d80000, 0x381174f008d80000, b"381174f008d80000", b"G", b"T"),
    (b"7", 7, 2288143, 0x0022ea0f, 0x08a00000, 0x3811750788a00000, b"3811750788a00000", b"C", b"A"),
    (b"7", 7, 2288144, 0x0022ea10, 0x08c00000, 0x3811750808c00000, b"3811750808c00000", b"G", b"A"),
    (b"7", 7, 2288159, 0x0022ea1f, 0x08e00000, 0x3811750f88e00000, b"3811750f88e00000", b"T", b"A"),
    (b"7", 7, 2288180, 0x0022ea34, 0x30cffc00, 0x3811751a30cffc00, b"3811751a30cffc00", b"GCTTTT", b"G"),
    (b"7", 7, 2288181, 0x0022ea35, 0x10ba0000, 0x3811751a90ba0000, b"3811751a90ba0000", b"CT", b"C"),
    (b"7", 7, 2288181, 0x0022ea35, 0x38bffe80, 0x3811751ab8bffe80, b"3811751ab8bffe80", b"CTTTTTT", b"C"),
    (b"7", 7, 2288181, 0x0022ea35, 0x18be8000, 0x3811751a98be8000, b"3811751a98be8000", b"CTT", b"C"),
    (b"7", 7, 2288181, 0x0022ea35, 0x38bffe80, 0x3811751ab8bffe80, b"3811751ab8bffe80", b"CTTTTTT", b"C"),
    (b"7", 7, 2288181, 0x0022ea35, 0x092e0000, 0x3811751a892e0000, b"3811751a892e0000", b"C", b"CT"),
    (b"8", 8, 167607, 0x00028eb7, 0x08c80000, 0x4001475b88c80000, b"4001475b88c80000", b"G", b"C"),
    (b"8", 8, 167613, 0x00028ebd, 0x08b80000, 0x4001475e88b80000, b"4001475e88b80000", b"C", b"T"),
    (b"8", 8, 167615, 0x00028ebf, 0x08b80000, 0x4001475f88b80000, b"4001475f88b80000", b"C", b"T"),
    (b"8", 8, 167632, 0x00028ed0, 0x08a00000, 0x4001476808a00000, b"4001476808a00000", b"C", b"A"),
    (b"8", 8, 167764, 0x00028f54, 0x18be8000, 0x400147aa18be8000, b"400147aa18be8000", b"CTT", b"C"),
    (b"8", 8, 167766, 0x00028f56, 0x08e00000, 0x400147ab08e00000, b"400147ab08e00000", b"T", b"A"),
    (b"8", 8, 167775, 0x00028f5f, 0x08e00000, 0x400147af88e00000, b"400147af88e00000", b"T", b"A"),
    (b"8", 8, 167780, 0x00028f64, 0x08f00000, 0x400147b208f00000, b"400147b208f00000", b"T", b"G"),
    (b"8", 8, 167800, 0x00028f78, 0x08e80000, 0x400147bc08e80000, b"400147bc08e80000", b"T", b"C"),
    (b"8", 8, 167809, 0x00028f81, 0x08c00000, 0x400147c088c00000, b"400147c088c00000", b"G", b"A"),
    (b"8", 8, 167814, 0x00028f86, 0x08a00000, 0x400147c308a00000, b"400147c308a00000", b"C", b"A"),
    (b"8", 8, 167821, 0x00028f8d, 0x08b80000, 0x400147c688b80000, b"400147c688b80000", b"C", b"T"),
    (b"8", 8, 167827, 0x00028f93, 0x4a7373c1, 0x400147c9ca7373c1, b"400147c9ca7373c1", b"CTTCCTGTCTTTATTTTGT", b"C"),
    (b"8", 8, 167839, 0x00028f9f, 0x08880000, 0x400147cf88880000, b"400147cf88880000", b"A", b"C"),
    (b"8", 8, 167839, 0x00028f9f, 0x10980000, 0x400147cf90980000, b"400147cf90980000", b"AT", b"A"),
    (b"8", 8, 167841, 0x00028fa1, 0x08f00000, 0x400147d088f00000, b"400147d088f00000", b"T", b"G"),
    (b"8", 8, 167871, 0x00028fbf, 0x08e80000, 0x400147df88e80000, b"400147df88e80000", b"T", b"C"),
    (b"8", 8, 167888, 0x00028fd0, 0x08e80000, 0x400147e808e80000, b"400147e808e80000", b"T", b"C"),
    (b"9", 9, 82863, 0x000143af, 0x08900000, 0x4800a1d788900000, b"4800a1d788900000", b"A", b"G"),
    (b"9", 9, 82869, 0x000143b5, 0x08c00000, 0x4800a1da88c00000, b"4800a1da88c00000", b"G", b"A"),
    (b"9", 9, 82893, 0x000143cd, 0x10ba0000, 0x4800a1e690ba0000, b"4800a1e690ba0000", b"CT", b"C"),
    (b"9", 9, 82940, 0x000143fc, 0x19fda000, 0x4800a1fe19fda000, b"4800a1fe19fda000", b"TTG", b"TCA"),
    (b"9", 9, 82940, 0x000143fc, 0x227ced00, 0x4800a1fe227ced00, b"4800a1fe227ced00", b"TTGC", b"TCGG"),
    (b"9", 9, 82941, 0x000143fd, 0x08e80000, 0x4800a1fe88e80000, b"4800a1fe88e80000", b"T", b"C"),
    (b"9", 9, 82943, 0x000143ff, 0x08b00000, 0x4800a1ff88b00000, b"4800a1ff88b00000", b"C", b"G"),
    (b"9", 9, 82998, 0x00014436, 0x08880000, 0x4800a21b08880000, b"4800a21b08880000", b"A", b"C"),
    (b"9", 9, 83006, 0x0001443e, 0x08980000, 0x4800a21f08980000, b"4800a21f08980000", b"A", b"T"),
    (b"9", 9, 83009, 0x00014441, 0x08a00000, 0x4800a22088a00000, b"4800a22088a00000", b"C", b"A"),
    (b"9", 9, 83020, 0x0001444c, 0x18df0000, 0x4800a22618df0000, b"4800a22618df0000", b"GTT", b"G"),
    (b"9", 9, 83021, 0x0001444d, 0x08e80000, 0x4800a22688e80000, b"4800a22688e80000", b"T", b"C"),
    (b"9", 9, 83037, 0x0001445d, 0x08900000, 0x4800a22e88900000, b"4800a22e88900000", b"A", b"G"),
    (b"9", 9, 83041, 0x00014461, 0x08980000, 0x4800a23088980000, b"4800a23088980000", b"A", b"T"),
    (b"9", 9, 83044, 0x00014464, 0x08c80000, 0x4800a23208c80000, b"4800a23208c80000", b"G", b"C"),
    (b"9", 9, 83045, 0x00014465, 0x0b56fa00, 0x4800a2328b56fa00, b"4800a2328b56fa00", b"G", b"GTCTTC"),
    (b"9", 9, 83046, 0x00014466, 0x09a98000, 0x4800a23309a98000, b"4800a23309a98000", b"C", b"CAT"),
    (b"9", 9, 83046, 0x00014466, 0x0a2a6000, 0x4800a2330a2a6000, b"4800a2330a2a6000", b"C", b"CCAT"),
    (b"9", 9, 83052, 0x0001446c, 0x08c80000, 0x4800a23608c80000, b"4800a23608c80000", b"G", b"C"),
    (b"10", 10, 102109, 0x00018edd, 0x08b80000, 0x5000c76e88b80000, b"5000c76e88b80000", b"C", b"T"),
    (b"10", 10, 102137, 0x00018ef9, 0x08a00000, 0x5000c77c88a00000, b"5000c77c88a00000", b"C", b"A"),
    (b"10", 10, 102149, 0x00018f05, 0x08a00000, 0x5000c78288a00000, b"5000c78288a00000", b"C", b"A"),
    (b"10", 10, 102177, 0x00018f21, 0x08e80000, 0x5000c79088e80000, b"5000c79088e80000", b"T", b"C"),
    (b"10", 10, 102180, 0x00018f24, 0x08b80000, 0x5000c79208b80000, b"5000c79208b80000", b"C", b"T"),
    (b"10", 10, 102251, 0x00018f6b, 0x08f00000, 0x5000c7b588f00000, b"5000c7b588f00000", b"T", b"G"),
    (b"10", 10, 102333, 0x00018fbd, 0x08b80000, 0x5000c7de88b80000, b"5000c7de88b80000", b"C", b"T"),
    (b"10", 10, 102352, 0x00018fd0, 0x08c00000, 0x5000c7e808c00000, b"5000c7e808c00000", b"G", b"A"),
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    (b"21", 21, 10800288, 0x00a4cca0, 0x08e00000, 0xa852665008e00000, b"a852665008e00000", b"T", b"A"),
    (b"21", 21, 10800297, 0x00a4cca9, 0x0b074400, 0xa85266548b074400, b"a85266548b074400", b"A", b"ATGGAG"),
    (b"21", 21, 10800297, 0x00a4cca9, 0x0b074400, 0xa85266548b074400, b"a85266548b074400", b"A", b"ATGGAG"),
    (b"21", 21, 10800298, 0x00a4ccaa, 0x0b7f4400, 0xa85266550b7f4400, b"a85266550b7f4400", b"T", b"TTGGAG"),
    (b"21", 21, 10800307, 0x00a4ccb3, 0x08c00000, 0xa852665988c00000, b"a852665988c00000", b"G", b"A"),
    (b"21", 21, 10800312, 0x00a4ccb8, 0x0b55d000, 0xa852665c0b55d000, b"a852665c0b55d000", b"G", b"GGTGGA"),
    (b"21", 21, 10800317, 0x00a4ccbd, 0x08900000, 0xa852665e88900000, b"a852665e88900000", b"A", b"G"),
    (b"21", 21, 10800320, 0x00a4ccc0, 0x17a5d0fb, 0xa852666017a5d0fb, b"a852666017a5d0fb", b"GAGTGGAATGGAATAGAGTGTAGTGAAATGC", b"G"),
    (b"21", 21, 10800322, 0x00a4ccc2, 0x10dc0000, 0xa852666110dc0000, b"a852666110dc0000", b"GT", b"G"),
    (b"21", 21, 10800334, 0x00a4ccce, 0x08900000, 0xa852666708900000, b"a852666708900000", b"A", b"G"),
    (b"21", 21, 10800357, 0x00a4cce5, 0x08900000, 0xa852667288900000, b"a852667288900000", b"A", b"G"),
    (b"21", 21, 10800364, 0x00a4ccec, 0x08c00000, 0xa852667608c00000, b"a852667608c00000", b"G", b"A"),
    (b"22", 22, 16471041, 0x00fb5401, 0x08a00000, 0xb07daa0088a00000, b"b07daa0088a00000", b"C", b"A"),
    (b"22", 22, 16471079, 0x00fb5427, 0x08a00000, 0xb07daa1388a00000, b"b07daa1388a00000", b"C", b"A"),
    (b"22", 22, 16471082, 0x00fb542a, 0x08b80000, 0xb07daa1508b80000, b"b07daa1508b80000", b"C", b"T"),
    (b"22", 22, 16471132, 0x00fb545c, 0x08f00000, 0xb07daa2e08f00000, b"b07daa2e08f00000", b"T", b"G"),
    (b"22", 22, 16471141, 0x00fb5465, 0x08c80000, 0xb07daa3288c80000, b"b07daa3288c80000", b"G", b"C"),
    (b"22", 22, 16471150, 0x00fb546e, 0x08e80000, 0xb07daa3708e80000, b"b07daa3708e80000", b"T", b"C"),
    (b"22", 22, 16471169, 0x00fb5481, 0x08d80000, 0xb07daa4088d80000, b"b07daa4088d80000", b"G", b"T"),
    (b"22", 22, 16471215, 0x00fb54af, 0x08980000, 0xb07daa5788980000, b"b07daa5788980000", b"A", b"T"),
    (b"22", 22, 16471224, 0x00fb54b8, 0x08e00000, 0xb07daa5c08e00000, b"b07daa5c08e00000", b"T", b"A"),
    (b"22", 22, 16471237, 0x00fb54c5, 0x08980000, 0xb07daa6288980000, b"b07daa6288980000", b"A", b"T"),
    (b"22", 22, 16471460, 0x00fb55a4, 0x08900000, 0xb07daad208900000, b"b07daad208900000", b"A", b"G"),
    (b"22", 22, 16471471, 0x00fb55af, 0x10980000, 0xb07daad790980000, b"b07daad790980000", b"AT", b"A"),
    (b"22", 22, 16471542, 0x00fb55f6, 0x08b80000, 0xb07daafb08b80000, b"b07daafb08b80000", b"C", b"T"),
    (b"22", 22, 16471543, 0x00fb55f7, 0x08900000, 0xb07daafb88900000, b"b07daafb88900000", b"A", b"G"),
    (b"22", 22, 16471660, 0x00fb566c, 0x10c40000, 0xb07dab3610c40000, b"b07dab3610c40000", b"GA", b"G"),
    (b"22", 22, 16471697, 0x00fb5691, 0x08f00000, 0xb07dab4888f00000, b"b07dab4888f00000", b"T", b"G"),
    (b"22", 22, 16471712, 0x00fb56a0, 0x08b80000, 0xb07dab5008b80000, b"b07dab5008b80000", b"C", b"T"),
    (b"22", 22, 16471823, 0x00fb570f, 0x08880000, 0xb07dab8788880000, b"b07dab8788880000", b"A", b"C"),
    (b"22", 22, 16471999, 0x00fb57bf, 0x08c00000, 0xb07dabdf88c00000, b"b07dabdf88c00000", b"G", b"A"),
    (b"22", 22, 16472177, 0x00fb5871, 0x08a00000, 0xb07dac3888a00000, b"b07dac3888a00000", b"C", b"A"),
    (b"22", 22, 16472753, 0x00fb5ab1, 0x08c00000, 0xb07dad5888c00000, b"b07dad5888c00000", b"G", b"A"),
    (b"22", 22, 16472816, 0x00fb5af0, 0x08e80000, 0xb07dad7808e80000, b"b07dad7808e80000", b"T", b"C"),
    (b"22", 22, 16473065, 0x00fb5be9, 0x08c00000, 0xb07dadf488c00000, b"b07dadf488c00000", b"G", b"A"),
    (b"22", 22, 16473366, 0x00fb5d16, 0x08c80000, 0xb07dae8b08c80000, b"b07dae8b08c80000", b"G", b"C"),
    (b"22", 22, 16473372, 0x00fb5d1c, 0x08c80000, 0xb07dae8e08c80000, b"b07dae8e08c80000", b"G", b"C"),
    (b"22", 22, 16473388, 0x00fb5d2c, 0x08c00000, 0xb07dae9608c00000, b"b07dae9608c00000", b"G", b"A"),
    (b"22", 22, 16473413, 0x00fb5d45, 0x08900000, 0xb07daea288900000, b"b07daea288900000", b"A", b"G"),
    (b"22", 22, 16473442, 0x00fb5d62, 0x08b80000, 0xb07daeb108b80000, b"b07daeb108b80000", b"C", b"T"),
    (b"22", 22, 16473456, 0x00fb5d70, 0x09020000, 0xb07daeb809020000, b"b07daeb809020000", b"A", b"AC"),
    (b"22", 22, 16473567, 0x00fb5ddf, 0x08b80000, 0xb07daeef88b80000, b"b07daeef88b80000", b"C", b"T"),
    (b"22", 22, 16473651, 0x00fb5e33, 0x08c00000, 0xb07daf1988c00000, b"b07daf1988c00000", b"G", b"A"),
    (b"22", 22, 16473654, 0x00fb5e36, 0x08980000, 0xb07daf1b08980000, b"b07daf1b08980000", b"A", b"T"),
    (b"X", 23, 2789116, 0x002a8efc, 0x08e80000, 0xb815477e08e80000, b"b815477e08e80000", b"T", b"C"),
    (b"X", 23, 2789137, 0x002a8f11, 0x08e80000, 0xb815478888e80000, b"b815478888e80000", b"T", b"C"),
    (b"X", 23, 2789141, 0x002a8f15, 0x08d80000, 0xb815478a88d80000, b"b815478a88d80000", b"G", b"T"),
    (b"X", 23, 2789146, 0x002a8f1a, 0x08900000, 0xb815478d08900000, b"b815478d08900000", b"A", b"G"),
    (b"X", 23, 2789155, 0x002a8f23, 0x08c80000, 0xb815479188c80000, b"b815479188c80000", b"G", b"C"),
    (b"X", 23, 2789163, 0x002a8f2b, 0x08d80000, 0xb815479588d80000, b"b815479588d80000", b"G", b"T"),
    (b"X", 23, 2789182, 0x002a8f3e, 0x08b00000, 0xb815479f08b00000, b"b815479f08b00000", b"C", b"G"),
    (b"X", 23, 2789191, 0x002a8f47, 0x08c00000, 0xb81547a388c00000, b"b81547a388c00000", b"G", b"A"),
    (b"X", 23, 2789209, 0x002a8f59, 0x48f5dd98, 0xb81547acc8f5dd98, b"b81547acc8f5dd98", b"TGGTGTGTA", b"T"),
    (b"X", 23, 2789229, 0x002a8f6d, 0x08b80000, 0xb81547b688b80000, b"b81547b688b80000", b"C", b"T"),
    (b"X", 23, 2789344, 0x002a8fe0, 0x08b80000, 0xb81547f008b80000, b"b81547f008b80000", b"C", b"T"),
    (b"X", 23, 2789360, 0x002a8ff0, 0x08b80000, 0xb81547f808b80000, b"b81547f808b80000", b"C", b"T"),
    (b"X", 23, 2789377, 0x002a9001, 0x08d80000, 0xb815480088d80000, b"b815480088d80000", b"G", b"T"),
    (b"X", 23, 2789384, 0x002a9008, 0x08f00000, 0xb815480408f00000, b"b815480408f00000", b"T", b"G"),
    (b"X", 23, 2789423, 0x002a902f, 0x08b80000, 0xb815481788b80000, b"b815481788b80000", b"C", b"T"),
    (b"X", 23, 2789427, 0x002a9033, 0x10e60000, 0xb815481990e60000, b"b815481990e60000", b"TA", b"T"),
    (b"X", 23, 2789427, 0x002a9033, 0x10e60000, 0xb815481990e60000, b"b815481990e60000", b"TA", b"T"),
    (b"X", 23, 2789531, 0x002a909b, 0x08b00000, 0xb815484d88b00000, b"b815484d88b00000", b"C", b"G"),
    (b"X", 23, 2789563, 0x002a90bb, 0x08a00000, 0xb815485d88a00000, b"b815485d88a00000", b"C", b"A"),
    (b"X", 23, 2789622, 0x002a90f6, 0x08b80000, 0xb815487b08b80000, b"b815487b08b80000", b"C", b"T"),
    (b"X", 23, 2789674, 0x002a912a, 0x08c00000, 0xb815489508c00000, b"b815489508c00000", b"G", b"A"),
    (b"X", 23, 2789684, 0x002a9134, 0x08c00000, 0xb815489a08c00000, b"b815489a08c00000", b"G", b"A"),
    (b"X", 23, 2789687, 0x002a9137, 0x08c00000, 0xb815489b88c00000, b"b815489b88c00000", b"G", b"A"),
    (b"X", 23, 2789724, 0x002a915c, 0x08b80000, 0xb81548ae08b80000, b"b81548ae08b80000", b"C", b"T"),
    (b"X", 23, 2789729, 0x002a9161, 0x219a0209, 0xb81548b0a19a0209, b"b81548b0a19a0209", b"CAAATAAATAAATAAAT", b"C"),
    (b"X", 23, 2789729, 0x002a9161, 0x383193ef, 0xb81548b0b83193ef, b"b81548b0b83193ef", b"CAAATAAATAAATAAATAAAT", b"C"),
    (b"X", 23, 2789729, 0x002a9161, 0x219a0209, 0xb81548b0a19a0209, b"b81548b0a19a0209", b"CAAATAAATAAATAAAT", b"C"),
    (b"X", 23, 2789729, 0x002a9161, 0x383193ef, 0xb81548b0b83193ef, b"b81548b0b83193ef", b"CAAATAAATAAATAAATAAAT", b"C"),
    (b"X", 23, 2789729, 0x002a9161, 0x219a0209, 0xb81548b0a19a0209, b"b81548b0a19a0209", b"CAAATAAATAAATAAAT", b"C"),
    (b"X", 23, 2789801, 0x002a91a9, 0x08b00000, 0xb81548d488b00000, b"b81548d488b00000", b"C", b"G"),
    (b"X", 23, 2789847, 0x002a91d7, 0x08f00000, 0xb81548eb88f00000, b"b81548eb88f00000", b"T", b"G"),
    (b"X", 23, 2789966, 0x002a924e, 0x08880000, 0xb815492708880000, b"b815492708880000", b"A", b"C"),
    (b"X", 23, 2789974, 0x002a9256, 0x08c00000, 0xb815492b08c00000, b"b815492b08c00000", b"G", b"A"),
    (b"Y", 24, 445728, 0x0006cd20, 0x08c00000, 0xc003669008c00000, b"c003669008c00000", b"G", b"A"),
    (b"Y", 24, 445771, 0x0006cd4b, 0x08900000, 0xc00366a588900000, b"c00366a588900000", b"A", b"G"),
    (b"Y", 24, 445773, 0x0006cd4d, 0x18840000, 0xc00366a698840000, b"c00366a698840000", b"AAG", b"A"),
    (b"Y", 24, 445779, 0x0006cd53, 0x08c00000, 0xc00366a988c00000, b"c00366a988c00000", b"G", b"A"),
    (b"Y", 24, 445786, 0x0006cd5a, 0x28c41000, 0xc00366ad28c41000, b"c00366ad28c41000", b"GAGAA", b"G"),
    (b"Y", 24, 445794, 0x0006cd62, 0x7f91cdb1, 0xc00366b17f91cdb1, b"c00366b17f91cdb1", b"AAGAAAGAAAG", b"A"),
    (b"Y", 24, 445797, 0x0006cd65, 0x08900000, 0xc00366b288900000, b"c00366b288900000", b"A", b"G"),
    (b"Y", 24, 445808, 0x0006cd70, 0x32728b71, 0xc00366b832728b71, b"c00366b832728b71", b"AAGAAAGAAAC", b"A"),
    (b"Y", 24, 445818, 0x0006cd7a, 0x28a00800, 0xc00366bd28a00800, b"c00366bd28a00800", b"CAAAA", b"C"),
    (b"Y", 24, 445821, 0x0006cd7d, 0x08900000, 0xc00366be88900000, b"c00366be88900000", b"A", b"G"),
    (b"Y", 24, 445832, 0x0006cd88, 0x08c00000, 0xc00366c408c00000, b"c00366c408c00000", b"G", b"A"),
    (b"Y", 24, 445850, 0x0006cd9a, 0x28804000, 0xc00366cd28804000, b"c00366cd28804000", b"AAAAG", b"A"),
    (b"Y", 24, 445876, 0x0006cdb4, 0x20d04000, 0xc00366da20d04000, b"c00366da20d04000", b"GGAA", b"G"),
    (b"Y", 24, 445890, 0x0006cdc2, 0x30c04400, 0xc00366e130c04400, b"c00366e130c04400", b"GAAAGA", b"G"),
    (b"Y", 24, 445897, 0x0006cdc9, 0x28844000, 0xc00366e4a8844000, b"c00366e4a8844000", b"AAGAG", b"A"),
    (b"Y", 24, 445919, 0x0006cddf, 0x08900000, 0xc00366ef88900000, b"c00366ef88900000", b"A", b"G"),
    (b"Y", 24, 445932, 0x0006cdec, 0x08c00000, 0xc00366f608c00000, b"c00366f608c00000", b"G", b"A"),
    (b"Y", 24, 445937, 0x0006cdf1, 0x28c41000, 0xc00366f8a8c41000, b"c00366f8a8c41000", b"GAGAA", b"G"),
    (b"Y", 24, 445948, 0x0006cdfc, 0x08980000, 0xc00366fe08980000, b"c00366fe08980000", b"A", b"T"),
    (b"Y", 24, 445955, 0x0006ce03, 0x18c10000, 0xc003670198c10000, b"c003670198c10000", b"GAA", b"G"),
    (b"Y", 24, 445957, 0x0006ce05, 0x08900000, 0xc003670288900000, b"c003670288900000", b"A", b"G"),
    (b"Y", 24, 445959, 0x0006ce07, 0x08c00000, 0xc003670388c00000, b"c003670388c00000", b"G", b"A"),
    (b"Y", 24, 445974, 0x0006ce16, 0x08900000, 0xc003670b08900000, b"c003670b08900000", b"A", b"G"),
    (b"Y", 24, 445977, 0x0006ce19, 0x18c10000, 0xc003670c98c10000, b"c003670c98c10000", b"GAA", b"G"),
    (b"Y", 24, 445978, 0x0006ce1a, 0x08900000, 0xc003670d08900000, b"c003670d08900000", b"A", b"G"),
    (b"Y", 24, 445978, 0x0006ce1a, 0x6842610d, 0xc003670d6842610d, b"c003670d6842610d", b"AAAGAAAGAAAGAAAGAAAG", b"A"),
    (b"Y", 24, 445997, 0x0006ce2d, 0x09500000, 0xc003671689500000, b"c003671689500000", b"G", b"GA"),
    (b"Y", 24, 446013, 0x0006ce3d, 0x08d80000, 0xc003671e88d80000, b"c003671e88d80000", b"G", b"T"),
    (b"Y", 24, 446014, 0x0006ce3e, 0x08900000, 0xc003671f08900000, b"c003671f08900000", b"A", b"G"),
    (b"Y", 24, 446018, 0x0006ce42, 0x08900000, 0xc003672108900000, b"c003672108900000", b"A", b"G"),
    (b"Y", 24, 446018, 0x0006ce42, 0x28814000, 0xc003672128814000, b"c003672128814000", b"AAAGG", b"A"),
    (b"Y", 24, 446022, 0x0006ce46, 0x08c00000, 0xc003672308c00000, b"c003672308c00000", b"G", b"A"),
    (b"Y", 24, 446054, 0x0006ce66, 0x08b80000, 0xc003673308b80000, b"c003673308b80000", b"C", b"T"),
    (b"Y", 24, 446055, 0x0006ce67, 0x08c00000, 0xc003673388c00000, b"c003673388c00000", b"G", b"A"),
    (b"chrMT", 25, 16305, 0x00003fb1, 0x08b80000, 0xc8001fd888b80000, b"c8001fd888b80000", b"C", b"T"),
    (b"CHRMT", 25, 16308, 0x00003fb4, 0x08900000, 0xc8001fda08900000, b"c8001fda08900000", b"A", b"G"),
    (b"MT", 25, 16310, 0x00003fb6, 0x08e80000, 0xc8001fdb08e80000, b"c8001fdb08e80000", b"T", b"C"),
    (b"MT", 25, 16318, 0x00003fbe, 0x08c00000, 0xc8001fdf08c00000, b"c8001fdf08c00000", b"G", b"A"),
    (b"MT", 25, 16319, 0x00003fbf, 0x08b80000, 0xc8001fdf88b80000, b"c8001fdf88b80000", b"C", b"T"),
    (b"MT", 25, 16324, 0x00003fc4, 0x08e80000, 0xc8001fe208e80000, b"c8001fe208e80000", b"T", b"C"),
    (b"MT", 25, 16326, 0x00003fc6, 0x08b80000, 0xc8001fe308b80000, b"c8001fe308b80000", b"C", b"T"),
    (b"MT", 25, 16331, 0x00003fcb, 0x08b80000, 0xc8001fe588b80000, b"c8001fe588b80000", b"C", b"T"),
    (b"MT", 25, 16336, 0x00003fd0, 0x08b80000, 0xc8001fe808b80000, b"c8001fe808b80000", b"C", b"T"),
    (b"MT", 25, 16343, 0x00003fd7, 0x08b80000, 0xc8001feb88b80000, b"c8001feb88b80000", b"C", b"T"),
    (b"MT", 25, 16344, 0x00003fd8, 0x08900000, 0xc8001fec08900000, b"c8001fec08900000", b"A", b"G"),
    (b"MT", 25, 16354, 0x00003fe2, 0x08b80000, 0xc8001ff108b80000, b"c8001ff108b80000", b"C", b"T"),
    (b"MT", 25, 16355, 0x00003fe3, 0x08e80000, 0xc8001ff188e80000, b"c8001ff188e80000", b"T", b"C"),
    (b"MT", 25, 16358, 0x00003fe6, 0x08e80000, 0xc8001ff308e80000, b"c8001ff308e80000", b"T", b"C"),
    (b"MT", 25, 16359, 0x00003fe7, 0x08b80000, 0xc8001ff388b80000, b"c8001ff388b80000", b"C", b"T"),
    (b"MT", 25, 16361, 0x00003fe9, 0x08e80000, 0xc8001ff488e80000, b"c8001ff488e80000", b"T", b"C"),
    (b"MT", 25, 16389, 0x00004005, 0x08c00000, 0xc800200288c00000, b"c800200288c00000", b"G", b"A"),
    (b"MT", 25, 16390, 0x00004006, 0x08c80000, 0xc800200308c80000, b"c800200308c80000", b"G", b"C"),
    (b"MT", 25, 16398, 0x0000400e, 0x08900000, 0xc800200708900000, b"c800200708900000", b"A", b"G"),
    (b"MT", 25, 16444, 0x0000403c, 0x08e80000, 0xc800201e08e80000, b"c800201e08e80000", b"T", b"C"),
    (b"MT", 25, 16498, 0x00004072, 0x08900000, 0xc800203908900000, b"c800203908900000", b"A", b"G"),
    (b"MT", 25, 16511, 0x0000407f, 0x08e80000, 0xc800203f88e80000, b"c800203f88e80000", b"T", b"C"),
    (b"MT", 25, 16518, 0x00004086, 0x08e80000, 0xc800204308e80000, b"c800204308e80000", b"T", b"C"),
    (b"MT", 25, 16527, 0x0000408f, 0x08b80000, 0xc800204788b80000, b"c800204788b80000", b"C", b"T"),
    (b"mt", 25, 16528, 0x00004090, 0x08e80000, 0xc800204808e80000, b"c800204808e80000", b"t", b"c"),
    (b"MT", 25, 19870, 0x00004d9e, 0x0d636362, 0xc80026cf0d636362, b"c80026cf0d636362", b"T", b"ACGTACGTAC"),
    (b"MT", 25, 19871, 0x00004d9f, 0x508d8d8e, 0xc80026cfd08d8d8e, b"c80026cfd08d8d8e", b"ACGTACGTAC", b"T"),
])


class TestFunctions(TestCase):

    @classmethod
    def setUpClass(cls):
        global npvk
        try:
            npvk = pyvk.VariantKey(
                os.path.realpath(os.path.dirname(os.path.realpath(__file__)) + "/../../c/test/data/genoref.bin"),
                os.path.realpath(os.path.dirname(os.path.realpath(__file__)) + "/../../c/test/data/nrvk.10.bin"),
                os.path.realpath(os.path.dirname(os.path.realpath(__file__)) + "/../../c/test/data/rsvk.10.bin"),
                os.path.realpath(os.path.dirname(os.path.realpath(__file__)) + "/../../c/test/data/vkrs.10.bin"))
        except Exception as err:
            assert False, "Unable to initialize the class: {0}".format(err)

    @classmethod
    def tearDownClass(cls):
        global npvk
        npvk.close()

    def test_encode_chrom(self):
        data = np.array([
            ["", "NA", "XY", "1X", "1Y", "1M", "1MT", "chr", " 1", "1 "],
            ["1", "01", "001", "0001", "chr1", "CHR1", "chr01", "CHR01", "chr001", "CHR001"],
            ["2", "02", "002", "0002", "chr2", "CHR2", "chr02", "CHR02", "chr002", "CHR002"],
            ["3", "03", "003", "0003", "chr3", "CHR3", "chr03", "CHR03", "chr003", "CHR003"],
            ["4", "04", "004", "0004", "chr4", "CHR4", "chr04", "CHR04", "chr004", "CHR004"],
            ["5", "05", "005", "0005", "chr5", "CHR5", "chr05", "CHR05", "chr005", "CHR005"],
            ["6", "06", "006", "0006", "chr6", "CHR6", "chr06", "CHR06", "chr006", "CHR006"],
            ["7", "07", "007", "0007", "chr7", "CHR7", "chr07", "CHR07", "chr007", "CHR007"],
            ["8", "08", "008", "0008", "chr8", "CHR8", "chr08", "CHR08", "chr008", "CHR008"],
            ["9", "09", "009", "0009", "chr9", "CHR9", "chr09", "CHR09", "chr009", "CHR009"],
            ["10", "010", "0010", "00010", "chr10", "CHR10", "chr010", "CHR010", "chr0010", "CHR0010"],
            ["11", "011", "0011", "00011", "chr11", "CHR11", "chr011", "CHR011", "chr0011", "CHR0011"],
            ["12", "012", "0012", "00012", "chr12", "CHR12", "chr012", "CHR012", "chr0012", "CHR0012"],
            ["13", "013", "0013", "00013", "chr13", "CHR13", "chr013", "CHR013", "chr0013", "CHR0013"],
            ["14", "014", "0014", "00014", "chr14", "CHR14", "chr014", "CHR014", "chr0014", "CHR0014"],
            ["15", "015", "0015", "00015", "chr15", "CHR15", "chr015", "CHR015", "chr0015", "CHR0015"],
            ["16", "016", "0016", "00016", "chr16", "CHR16", "chr016", "CHR016", "chr0016", "CHR0016"],
            ["17", "017", "0017", "00017", "chr17", "CHR17", "chr017", "CHR017", "chr0017", "CHR0017"],
            ["18", "018", "0018", "00018", "chr18", "CHR18", "chr018", "CHR018", "chr0018", "CHR0018"],
            ["19", "019", "0019", "00019", "chr19", "CHR19", "chr019", "CHR019", "chr0019", "CHR0019"],
            ["20", "020", "0020", "00020", "chr20", "CHR20", "chr020", "CHR020", "chr0020", "CHR0020"],
            ["21", "021", "0021", "00021", "chr21", "CHR21", "chr021", "CHR021", "chr0021", "CHR0021"],
            ["22", "022", "0022", "00022", "chr22", "CHR22", "chr022", "CHR022", "chr0022", "CHR0022"],
            ["X", "x", "chrX", "chrx", "CHRX", "CHRx", "X", "X", "X", "X"],
            ["Y", "y", "chrY", "chry", "CHRY", "CHRy", "Y", "Y", "Y", "Y"],
            ["M", "m", "MT", "mt", "chrM", "chrm", "chrMT", "chrmt", "CHRMt", "CHRmT"],
        ])
        for i in range(0, 26):
            e = np.repeat(i, 10)
            c = npvk.encode_chrom(data[i])
            np.testing.assert_array_equal(c, e)
        chrom = npvk.encode_chrom(b"WRONG")
        self.assertEqual(chrom, 0)

    def test_encode_chrom_input_type(self):
        self.assertEqual(npvk.encode_chrom(b"chr01"), npvk.encode_chrom("chr01"))

    def test_decode_chrom(self):
        code = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]
        e = np.array([b"NA", b"1", b"2", b"3", b"4", b"5", b"6", b"7", b"8", b"9", b"10", b"11", b"12", b"13", b"14", b"15", b"16", b"17", b"18", b"19", b"20", b"21", b"22", b"X", b"Y", b"MT"], dtype='|S2')
        c = npvk.decode_chrom(code)
        np.testing.assert_array_equal(c, e)

    def test_encode_refalt_input_type(self):
        self.assertEqual(npvk.encode_refalt(b"AC", b"GT"), npvk.encode_refalt("AC", "GT"))
        self.assertEqual(npvk.encode_refalt(b"ACGTACGT", b"GTACGTAC"), npvk.encode_refalt("ACGTACGT", "GTACGTAC"))

    def test_encode_refalt(self):
        base = [b"A", b"C", b"N", b"GT", b"ACG", b"ACGTa", b"ACGTac", b"ACGTacg", b"ACGTacgt", b"ACGTACGTAC", b"ACGTacgtACGT"]
        e = np.array([
            142606336,  142606336,  143130624,  144703488,  726812453,  330097465,
            152436736,  282591232,  159580160,  411828224,  176381952,  680361984,
            184771072,  814581760,  193159936,  948800512,  201548640, 1083018624,
            218325858, 1351454088, 1057675291, 1369359907,  145227776,  145227776,
            1375594857, 1513805153,  154533888,  282722304,  161677312,  411860992,
            178479104,  680364032,  186868224,  814582272,  195257088,  948800640,
            203645792, 1083018656,  220423010, 1351454090, 1398628389, 1358766431,
            1969243823, 1969243823,  971081273, 1771898065,  776945419, 1002621441,
            1754088851, 1261827981, 1010241683, 1792303827, 1458585093, 1889528781,
            273848339, 1684605733, 1654748801, 1190621367,  785406155, 2000763481,
            291340288,  291340288,  299417600,  420306944,  316200960,  688756224,
            324589696,  822971776,  332978368,  957189472,  341367000, 1091407320,
            636483075, 1776551723, 1695405603, 1483277935,  428617728,  428617728,
            445396480,  697139968,  453785120,  831359168,  462173744,  965577776,
            470562358, 1099795852,  191755869, 1887943745, 1415691159,  303875507,
            713917280,  713917280,  722305890,  848136408,  723621645, 1783965747,
            508782503,  458890457,  581191723,  141156817, 1430489581,  628679603,
            1225091505, 1225091505, 1071275181, 1218465497, 1052062435,  681734883,
            1735823055, 1173846073,  528456553, 1747209651,  859706021,  859706021,
            1597496643, 1378980139, 1362028185, 1471164791, 1267233551,  573285289,
            284858523,  284858523, 1987610005,  378861315,  644679011,  912925615,
            1451695617, 1451695617, 1610695323, 2076346979,  976842551,  976842551,
        ], dtype=np.uint32)
        iref = []
        ialt = []
        for i in range(0, 11):
            for j in range(i, 11):
                ri = i
                rj = j
                for r in range(0, 2):
                    iref.append(base[ri])
                    ialt.append(base[rj])
                    tmp = ri
                    ri = rj
                    rj = tmp
        h = npvk.encode_refalt(iref, ialt)
        np.testing.assert_array_equal(h, e)

    def test_decode_refalt(self):
        d = np.array([
            142606336,  142606336,  143130624,  144703488,  726812453,  330097465,
            152436736,  282591232,  159580160,  411828224,  176381952,  680361984,
            184771072,  814581760,  193159936,  948800512,  201548640, 1083018624,
            218325858, 1351454088, 1057675291, 1369359907,  145227776,  145227776,
            1375594857, 1513805153,  154533888,  282722304,  161677312,  411860992,
            178479104,  680364032,  186868224,  814582272,  195257088,  948800640,
            203645792, 1083018656,  220423010, 1351454090, 1398628389, 1358766431,
            1969243823, 1969243823,  971081273, 1771898065,  776945419, 1002621441,
            1754088851, 1261827981, 1010241683, 1792303827, 1458585093, 1889528781,
            273848339, 1684605733, 1654748801, 1190621367,  785406155, 2000763481,
            291340288,  291340288,  299417600,  420306944,  316200960,  688756224,
            324589696,  822971776,  332978368,  957189472,  341367000, 1091407320,
            636483075, 1776551723, 1695405603, 1483277935,  428617728,  428617728,
            445396480,  697139968,  453785120,  831359168,  462173744,  965577776,
            470562358, 1099795852,  191755869, 1887943745, 1415691159,  303875507,
            713917280,  713917280,  722305890,  848136408,  723621645, 1783965747,
            508782503,  458890457,  581191723,  141156817, 1430489581,  628679603,
            1225091505, 1225091505, 1071275181, 1218465497, 1052062435,  681734883,
            1735823055, 1173846073,  528456553, 1747209651,  859706021,  859706021,
            1597496643, 1378980139, 1362028185, 1471164791, 1267233551,  573285289,
            284858523,  284858523, 1987610005,  378861315,  644679011,  912925615,
            1451695617, 1451695617, 1610695323, 2076346979,  976842551,  976842551,
        ], dtype=np.uint32)
        eref = np.array([b'A', b'A', b'A', b'C', b'', b'', b'A', b'GT', b'A', b'ACG', b'A', b'ACGTA', b'A',
                         b'ACGTAC', b'A', b'ACGTACG', b'A', b'ACGTACGT', b'A', b'ACGTACGTAC', b'', b'',
                         b'C', b'C', b'', b'', b'C', b'GT', b'C', b'ACG', b'C', b'ACGTA', b'C', b'ACGTAC',
                         b'C', b'ACGTACG', b'C', b'ACGTACGT', b'C', b'ACGTACGTAC', b'', b'', b'', b'', b'',
                         b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'GT', b'GT',
                         b'GT', b'ACG', b'GT', b'ACGTA', b'GT', b'ACGTAC', b'GT', b'ACGTACG', b'GT',
                         b'ACGTACGT', b'', b'', b'', b'', b'ACG', b'ACG', b'ACG', b'ACGTA', b'ACG',
                         b'ACGTAC', b'ACG', b'ACGTACG', b'ACG', b'ACGTACGT', b'', b'', b'', b'', b'ACGTA',
                         b'ACGTA', b'ACGTA', b'ACGTAC', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'',
                         b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'',
                         b'', b'', b'', b'', b'', b'', b'', b'', b''], dtype=np.string_)
        ealt = np.array([b'A', b'A', b'C', b'A', b'', b'', b'GT', b'A', b'ACG', b'A', b'ACGTA', b'A',
                         b'ACGTAC', b'A', b'ACGTACG', b'A', b'ACGTACGT', b'A', b'ACGTACGTAC', b'A', b'',
                         b'', b'C', b'C', b'', b'', b'GT', b'C', b'ACG', b'C', b'ACGTA', b'C', b'ACGTAC', b'C',
                         b'ACGTACG', b'C', b'ACGTACGT', b'C', b'ACGTACGTAC', b'C', b'', b'', b'', b'', b'',
                         b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'GT', b'GT',
                         b'ACG', b'GT', b'ACGTA', b'GT', b'ACGTAC', b'GT', b'ACGTACG', b'GT', b'ACGTACGT',
                         b'GT', b'', b'', b'', b'', b'ACG', b'ACG', b'ACGTA', b'ACG', b'ACGTAC', b'ACG',
                         b'ACGTACG', b'ACG', b'ACGTACGT', b'ACG', b'', b'', b'', b'', b'ACGTA', b'ACGTA',
                         b'ACGTAC', b'ACGTA', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'',
                         b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'',
                         b'', b'', b'', b'', b'', b'', b''], dtype=np.string_)
        esizeref = np.array([1, 1, 1, 1, 0, 0, 1, 2, 1, 3, 1, 5, 1, 6, 1, 7, 1, 8, 1, 10, 0, 0, 1, 1,
                             0, 0, 1, 2, 1, 3, 1, 5, 1, 6, 1, 7, 1, 8, 1, 10, 0, 0, 0, 0, 0, 0, 0, 0,
                             0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 2, 3, 2, 5, 2, 6, 2, 7, 2, 8,
                             0, 0, 0, 0, 3, 3, 3, 5, 3, 6, 3, 7, 3, 8, 0, 0, 0, 0, 5, 5, 5, 6, 0, 0,
                             0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
                             0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], dtype=np.uint8)
        esizealt = np.array([1, 1, 1, 1, 0, 0, 2, 1, 3, 1, 5, 1, 6, 1, 7, 1, 8, 1, 10, 1, 0, 0, 1, 1,
                             0, 0, 2, 1, 3, 1, 5, 1, 6, 1, 7, 1, 8, 1, 10, 1, 0, 0, 0, 0, 0, 0, 0, 0,
                             0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 3, 2, 5, 2, 6, 2, 7, 2, 8, 2,
                             0, 0, 0, 0, 3, 3, 5, 3, 6, 3, 7, 3, 8, 3, 0, 0, 0, 0, 5, 5, 6, 5, 0, 0,
                             0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
                             0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], dtype=np.uint8)
        ref, alt, sizeref, sizealt = npvk.decode_refalt(d)
        np.testing.assert_array_equal(ref, eref)
        np.testing.assert_array_equal(alt, ealt)
        np.testing.assert_array_equal(sizeref, esizeref)
        np.testing.assert_array_equal(sizealt, esizealt)

    def test_encode_variantkey(self):
        h = npvk.encode_variantkey(vtd[:, 1], vtd[:, 3], vtd[:, 4])
        np.testing.assert_array_equal(h, vtd[:, 5].astype(np.uint64))

    def test_extract_variantkey_chrom(self):
        h = npvk.extract_variantkey_chrom(vtd[:, 5].astype(np.uint64))
        np.testing.assert_array_equal(h, vtd[:, 1].astype(np.uint8))

    def test_extract_variantkey_pos(self):
        h = npvk.extract_variantkey_pos(vtd[:, 5].astype(np.uint64))
        np.testing.assert_array_equal(h, vtd[:, 3].astype(np.uint32))

    def test_extract_variantkey_refalt(self):
        h = npvk.extract_variantkey_refalt(vtd[:, 5].astype(np.uint64))
        np.testing.assert_array_equal(h, vtd[:, 4].astype(np.uint32))

    def test_decode_variantkey(self):
        c, p, r = npvk.decode_variantkey(vtd[:, 5].astype(np.uint64))
        np.testing.assert_array_equal(c, vtd[:, 1].astype(np.uint8))
        np.testing.assert_array_equal(p, vtd[:, 3].astype(np.uint32))
        np.testing.assert_array_equal(r, vtd[:, 4].astype(np.uint32))

    def test_variantkey(self):
        h = npvk.variantkey(vtd[:, 0], vtd[:, 2], vtd[:, 7], vtd[:, 8])
        np.testing.assert_array_equal(h, vtd[:, 5].astype(np.uint64))

    def test_variantkey_range(self):
        # 0:chrom, 1:pos_min, 2:pos_max, 3:vk_min, 4:vk_max
        d = np.array([
            (1, 0, 268435455, 0x0800000000000000, 0x0fffffffffffffff),
            (2, 268435454, 268435455, 0x17ffffff00000000, 0x17ffffffffffffff),
            (3, 0, 1, 0x1800000000000000, 0x18000000ffffffff),
            (4, 1000169, 267435286, 0x2007a17480000000, 0x27f85e8b7fffffff),
            (5, 2000338, 2050373, 0x280f42e900000000, 0x280fa4a2ffffffff),
            (6, 3000507, 3060549, 0x3016e45d80000000, 0x301759a2ffffffff),
            (7, 4000676, 4070725, 0x381e85d200000000, 0x381f0ea2ffffffff),
            (8, 5000845, 5080901, 0x4026274680000000, 0x4026c3a2ffffffff),
            (9, 6001014, 6091077, 0x482dc8bb00000000, 0x482e78a2ffffffff),
            (10, 7001183, 7101253, 0x50356a2f80000000, 0x50362da2ffffffff),
            (11, 8001352, 8111429, 0x583d0ba400000000, 0x583de2a2ffffffff),
            (12, 9001521, 9121605, 0x6044ad1880000000, 0x604597a2ffffffff),
            (13, 10001690, 10131781, 0x684c4e8d00000000, 0x684d4ca2ffffffff),
            (14, 11001859, 11141957, 0x7053f00180000000, 0x705501a2ffffffff),
            (15, 12002028, 12152133, 0x785b917600000000, 0x785cb6a2ffffffff),
            (16, 13002197, 13162309, 0x806332ea80000000, 0x80646ba2ffffffff),
            (17, 14002366, 14172485, 0x886ad45f00000000, 0x886c20a2ffffffff),
            (18, 15002535, 15182661, 0x907275d380000000, 0x9073d5a2ffffffff),
            (19, 16002704, 16192837, 0x987a174800000000, 0x987b8aa2ffffffff),
            (20, 17002873, 17203013, 0xa081b8bc80000000, 0xa0833fa2ffffffff),
            (21, 18003042, 18213189, 0xa8895a3100000000, 0xa88af4a2ffffffff),
            (22, 19003211, 19223365, 0xb090fba580000000, 0xb092a9a2ffffffff),
            (23, 20003380, 20233541, 0xb8989d1a00000000, 0xb89a5ea2ffffffff),
            (24, 21003549, 21243717, 0xc0a03e8e80000000, 0xc0a213a2ffffffff),
            (25, 22003718, 268435455, 0xc8a7e00300000000, 0xcfffffffffffffff),
        ], dtype=np.uint64)
        vkmin, vkmax = npvk.variantkey_range(d[:, 0], d[:, 1], d[:, 2])
        np.testing.assert_array_equal(vkmin, d[:, 3].astype(np.uint64))
        np.testing.assert_array_equal(vkmax, d[:, 4].astype(np.uint64))

    def test_compare_variantkey_chrom(self):
        d = np.array([
            (0x08027a3c08e80000, 0x100036cc08900000, -1),
            (0x0fffffff88b80000, 0x08027a2188c80000, 0),
            (0x100036cc08900000, 0x08027a3c08e80000, 1),
        ])
        res = npvk.compare_variantkey_chrom(d[:, 0], d[:, 1])
        np.testing.assert_array_equal(res, d[:, 2].astype(np.int_))

    def test_compare_variantkey_chrom_pos(self):
        d = np.array([
            (0x08027a3c08e80000, 0x100036cc08900000, -1),
            (0x100036cc08900000, 0x08027a3c08e80000, 1),
            (0x08027a2588b00000, 0x0fffffff88b80000, -1),
            (0x0fffffff88b80000, 0x0fffffff8ae2503b, 0),
            (0x0fffffff88b80000, 0x08027a2588b00000, 1),
        ])
        res = npvk.compare_variantkey_chrom_pos(d[:, 0], d[:, 1])
        np.testing.assert_array_equal(res, d[:, 2].astype(np.int_))

    def test_variantkey_hex(self):
        h = npvk.variantkey_hex(vtd[:, 5])
        np.testing.assert_array_equal(h, vtd[:, 6].astype(np.string_))

    def test_parse_variantkey_hex(self):
        h = npvk.parse_variantkey_hex(vtd[:, 6])
        np.testing.assert_array_equal(h, vtd[:, 5].astype(np.uint64))

    def test_parse_variantkey_hex_input_type(self):
        self.assertEqual(npvk.parse_variantkey_hex(b"b815481990e60000"), npvk.parse_variantkey_hex("b815481990e60000"))