Merge pull request #55 from 4dn-dcic/0.3.5

0.3.5
4dn-dcic · Mar 21, 2018 · 9e0d8cc · 9e0d8cc
2 parents a181178 + b6312ff
commit 9e0d8cc
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diff --git a/.travis.yml b/.travis.yml
@@ -1,23 +1,33 @@
-language: c python
-sudo: required
-compiler: gcc
-python:
-- '3.6'
-- '2.7'
-env:
-- VALGRIND_TEST_ON=1
-before_install:
-- sudo apt-get install -qq valgrind
-script:
-- make
-- |
-  if [[ $TRAVIS_PYTHON_VERSION == 3.6 ]]; then
-  sudo python3 setup.py install
-  python3 test/test.py
-  fi
-- |
-  if [[ $TRAVIS_PYTHON_VERSION == 2.7 ]]; then
-  sudo python setup.py install
-  python test/test.py
-  fi
-- source test/test_c.sh  # valgrind test is applied when VALGRIND_TEST_ON=1
+matrix:
+  include:
+    - language: c
+      sudo: required
+      compiler: gcc
+      env:
+      - VALGRIND_TEST_ON=1
+      before_install:
+      - sudo apt-get install -qq valgrind
+      - sudo apt-get update
+      - sudo apt-get install python2.7
+      script:
+      - make
+      - sudo python setup.py install
+      - python test/test.py
+      - python test/test_oldindex.py
+      - source test/test_c.sh  # valgrind test is applied when VALGRIND_TEST_ON=1
+      - source test/test_c_oldindex.sh  # test for old index
+    - language: c
+      sudo: required
+      compiler: gcc
+      env:
+      - VALGRIND_TEST_ON=1
+      before_install:
+      - sudo apt-get install -qq valgrind
+      - sudo apt-get update
+      - sudo apt-get install python3
+      - sudo apt-get install python3-setuptools
+      script:
+      - make
+      - sudo python3 setup.py install
+      - python3 test/test.py
+      - python3 test/test_oldindex.py
diff --git a/README.md b/README.md
@@ -639,6 +639,9 @@ ulimit -n 2000
 
 ## Version history
 
+### 0.3.5
+* Backward compatibility is added - The index generated by the previous version (0.2.5 ~ 0.3.3) can now be auto-detected and used by Pairix.
+
 ### 0.3.4
 * The maximum chromosome size allowed is now 2^30 instead of 2^29 with new index. *Index structure changed.*
 

diff --git a/VERSION.txt b/VERSION.txt
@@ -1 +1 @@
-0.3.4
+0.3.5
diff --git a/samples/SRR1171591.variants.snp.vqsr.p.vcf.gz.px2 b/samples/SRR1171591.variants.snp.vqsr.p.vcf.gz.px2
diff --git a/samples/merged_nodups.space.chrblock_sorted.subsample1.txt.gz.px2 b/samples/merged_nodups.space.chrblock_sorted.subsample1.txt.gz.px2
diff --git a/samples/old_index/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz b/samples/old_index/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz
diff --git a/samples/old_index/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz.px2 b/samples/old_index/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz.px2
diff --git a/samples/old_index/4dn.bsorted.chr21_22_only.pairs.gz b/samples/old_index/4dn.bsorted.chr21_22_only.pairs.gz
diff --git a/samples/old_index/4dn.bsorted.chr21_22_only.pairs.gz.px2 b/samples/old_index/4dn.bsorted.chr21_22_only.pairs.gz.px2
diff --git a/samples/old_index/SRR1171591.variants.snp.vqsr.p.vcf.gz b/samples/old_index/SRR1171591.variants.snp.vqsr.p.vcf.gz
diff --git a/samples/old_index/SRR1171591.variants.snp.vqsr.p.vcf.gz.px2 b/samples/old_index/SRR1171591.variants.snp.vqsr.p.vcf.gz.px2
diff --git a/samples/old_index/hg19.chrom.sizes.-chr b/samples/old_index/hg19.chrom.sizes.-chr
@@ -0,0 +1,24 @@
+1	249250621
+2	243199373
+3	198022430
+4	191154276
+5	180915260
+6	171115067
+7	159138663
+X	155270560
+8	146364022
+9	141213431
+10	135534747
+11	135006516
+12	133851895
+13	115169878
+14	107349540
+15	102531392
+16	90354753
+17	81195210
+18	78077248
+20	63025520
+Y	59373566
+19	59128983
+22	51304566
+21	48129895
diff --git a/samples/old_index/hg19.chrom.sizes.chr21_22_only b/samples/old_index/hg19.chrom.sizes.chr21_22_only
@@ -0,0 +1,2 @@
+chr21	48129895
+chr22	51304566