Week04 HW -DONE! ha

LICENSE

@@ -1,10 +1,16 @@
+<<<<<<< HEAD
 UC Copyright Notice
 
 This software is Copyright (C) 2015 The Regents of the University of California. All Rights Reserved.
 
 Permission to copy, modify, and distribute this software and its documentation for educational,
 research and non-profit purposes, without fee, and without a written agreement is hereby granted,
 provided that the above copyright notice, this paragraph and the following three paragraphs appear in all copies.
+=======
+This software is Copyright © 2016 The Regents of the University of California. All Rights Reserved.
+
+Permission to use, copy, modify, and distribute this software and its documentation for educational, research and non-profit purposes, without fee, and without a written agreement is hereby granted, provided that the above copyright notice, this paragraph and the following three paragraphs appear in all copies.
+>>>>>>> e41c1b482de2e729f7b4e7cb20fa8f28575a5152
 
 Permission to make commercial use of this software may be obtained by contacting:
 Technology Transfer Office
@@ -14,6 +20,7 @@ La Jolla, CA 92093-0910
 (858) 534-5815
 invent@ucsd.edu
 
+<<<<<<< HEAD
 This software program and documentation are copyrighted by The Regents of the
 University of California. The software program and documentation are supplied
 "as is", without any accompanying services from The Regents. The Regents does
@@ -35,3 +42,8 @@ THE SOFTWARE PROVIDED HEREUNDER IS ON AN "AS IS" BASIS,
 AND THE UNIVERSITY OF CALIFORNIA HAS NO OBLIGATIONS TO
 PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR
 MODIFICATIONS.
+=======
+This software program and documentation are copyrighted by The Regents of the University of California. The software program and documentation are supplied "as is", without any accompanying services from The Regents. The Regents does not warrant that the operation of the program will be uninterrupted or error-free. The end-user understands that the program was developed for research purposes and is advised not to rely exclusively on the program for any reason.
+
+IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. THE UNIVERSITY OF CALIFORNIA SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE UNIVERSITY OF CALIFORNIA HAS NO OBLIGATIONS TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
+>>>>>>> e41c1b482de2e729f7b4e7cb20fa8f28575a5152

README.md

@@ -1,3 +1,4 @@
+<<<<<<< HEAD
 [![Build Status](https://travis-ci.org/biom262/biom262-2016.svg?branch=master)](https://travis-ci.org/biom262/biom262-2016) [![Join the chat at https://gitter.im/biom262/biom262-2016](https://badges.gitter.im/biom262/biom262-2016.svg)](https://gitter.im/biom262/biom262-2016?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 
 
@@ -43,3 +44,7 @@ git remote add upstream https://github.com/biom262/biom262-2016
 ```
 
 ***Note: you will still need to create  a branch named after the week***
+=======
+# biom262-hw1
+Biom262 Week 1 Homework for Tim Shaw and Ben Lewis
+>>>>>>> e41c1b482de2e729f7b4e7cb20fa8f28575a5152

hg19.genome

@@ -0,0 +1,94 @@
+chrom	size
+chr1	249250621
+chr2	243199373
+chr3	198022430
+chr4	191154276
+chr5	180915260
+chr6	171115067
+chr7	159138663
+chrX	155270560
+chr8	146364022
+chr9	141213431
+chr10	135534747
+chr11	135006516
+chr12	133851895
+chr13	115169878
+chr14	107349540
+chr15	102531392
+chr16	90354753
+chr17	81195210
+chr18	78077248
+chr20	63025520
+chrY	59373566
+chr19	59128983
+chr22	51304566
+chr21	48129895
+chr6_ssto_hap7	4928567
+chr6_mcf_hap5	4833398
+chr6_cox_hap2	4795371
+chr6_mann_hap4	4683263
+chr6_apd_hap1	4622290
+chr6_qbl_hap6	4611984
+chr6_dbb_hap3	4610396
+chr17_ctg5_hap1	1680828
+chr4_ctg9_hap1	590426
+chr1_gl000192_random	547496
+chrUn_gl000225	211173
+chr4_gl000194_random	191469
+chr4_gl000193_random	189789
+chr9_gl000200_random	187035
+chrUn_gl000222	186861
+chrUn_gl000212	186858
+chr7_gl000195_random	182896
+chrUn_gl000223	180455
+chrUn_gl000224	179693
+chrUn_gl000219	179198
+chr17_gl000205_random	174588
+chrUn_gl000215	172545
+chrUn_gl000216	172294
+chrUn_gl000217	172149
+chr9_gl000199_random	169874
+chrUn_gl000211	166566
+chrUn_gl000213	164239
+chrUn_gl000220	161802
+chrUn_gl000218	161147
+chr19_gl000209_random	159169
+chrUn_gl000221	155397
+chrUn_gl000214	137718
+chrUn_gl000228	129120
+chrUn_gl000227	128374
+chr1_gl000191_random	106433
+chr19_gl000208_random	92689
+chr9_gl000198_random	90085
+chr17_gl000204_random	81310
+chrUn_gl000233	45941
+chrUn_gl000237	45867
+chrUn_gl000230	43691
+chrUn_gl000242	43523
+chrUn_gl000243	43341
+chrUn_gl000241	42152
+chrUn_gl000236	41934
+chrUn_gl000240	41933
+chr17_gl000206_random	41001
+chrUn_gl000232	40652
+chrUn_gl000234	40531
+chr11_gl000202_random	40103
+chrUn_gl000238	39939
+chrUn_gl000244	39929
+chrUn_gl000248	39786
+chr8_gl000196_random	38914
+chrUn_gl000249	38502
+chrUn_gl000246	38154
+chr17_gl000203_random	37498
+chr8_gl000197_random	37175
+chrUn_gl000245	36651
+chrUn_gl000247	36422
+chr9_gl000201_random	36148
+chrUn_gl000235	34474
+chrUn_gl000239	33824
+chr21_gl000210_random	27682
+chrUn_gl000231	27386
+chrUn_gl000229	19913
+chrM	16571
+chrUn_gl000226	15008
+chr18_gl000207_random	4262