Merge pull request #3 from masarunakajima/cleanup-format-reads

Cleanup format reads

Author: masarunakajima

Makefile.am

@@ -16,7 +16,7 @@
 
 EXTRA_DIST = \
              README.md \
-	     LICENSE \
+             LICENSE \
              docs/README.md \
              docs/mkdocs.yml \
              docs/content/abismal.md \
@@ -57,6 +57,7 @@ EXTRA_DIST = \
              pipeline/runconfig.yaml \
              pipeline/Snakefile \
              data/tRex1.fa \
+             data/tRex1_promoters.bed \
              data/reads_1.fq.gz \
              data/reads_2.fq.gz \
              data/md5sum.txt \
@@ -70,7 +71,8 @@ EXTRA_DIST = \
              test_scripts/test_levels.test \
              test_scripts/test_sym.test \
              test_scripts/test_hmr.test \
-	     test_scripts/test_roi.test
+             test_scripts/test_roi.test \
+             test_scripts/test_selectsites.test
 
 ### ADS: the file md5sum.txt can be regenerated by running the tests
 ### with "make check" and then doing `md5sum tests/* > md5sum.txt`
@@ -85,16 +87,17 @@ AM_CPPFLAGS = -I $(top_srcdir)/src/common -I $(top_srcdir)/src/smithlab_cpp
 CXXFLAGS = -Wall -O3 $(OPENMP_CXXFLAGS) # default has optimization on
 
 TESTS = test_scripts/test_simreads.test \
-	test_scripts/test_abismalidx.test \
-	test_scripts/test_abismal.test \
-	test_scripts/test_format.test \
-	test_scripts/test_uniq.test \
-	test_scripts/test_bsrate.test \
-	test_scripts/test_counts.test \
-	test_scripts/test_levels.test \
-	test_scripts/test_sym.test \
-	test_scripts/test_hmr.test \
-	test_scripts/test_roi.test
+        test_scripts/test_abismalidx.test \
+        test_scripts/test_abismal.test \
+        test_scripts/test_format.test \
+        test_scripts/test_uniq.test \
+        test_scripts/test_bsrate.test \
+        test_scripts/test_counts.test \
+        test_scripts/test_levels.test \
+        test_scripts/test_sym.test \
+        test_scripts/test_hmr.test \
+        test_scripts/test_roi.test \
+        test_scripts/test_selectsites.test 
 
 TEST_EXTENSIONS = .test
 
@@ -104,6 +107,7 @@ test_scripts/test_uniq.log: test_scripts/test_format.log
 test_scripts/test_bsrate.log: test_scripts/test_uniq.log
 test_scripts/test_counts.log: test_scripts/test_uniq.log
 test_scripts/test_levels.log: test_scripts/test_counts.log
+test_scripts/test_selectsites.log: test_scripts/test_counts.log
 test_scripts/test_sym.log: test_scripts/test_counts.log
 test_scripts/test_hmr.log: test_scripts/test_sym.log
 test_scripts/test_roi.log: test_scripts/test_sym.log
@@ -188,18 +192,19 @@ dnmtools_SOURCES += src/mlml/mlml.cpp
 ## grep "^outfile" test_scripts/*.test
 ##
 CLEANFILES = \
-	tests/reads.bsrate \
-	tests/reads.counts \
-	tests/reads.counts.sym \
-	tests/reads.fmt.sam \
-	tests/reads.fmt.srt.sam \
-	tests/reads.fmt.srt.uniq.sam \
-	tests/reads.hmr \
-	tests/reads.levels \
-	tests/reads.mstats \
-	tests/reads.sam \
-	tests/reads.ustats \
-	tests/simreads_1.fq \
-	tests/simreads_2.fq \
-	tests/tRex1.idx \
-	tests/tRex1_promoters.roi.bed
+    tests/reads.bsrate \
+    tests/reads.counts \
+    tests/reads.counts.sym \
+    tests/reads.fmt.sam \
+    tests/reads.fmt.srt.sam \
+    tests/reads.fmt.srt.uniq.sam \
+    tests/reads.hmr \
+    tests/reads.levels \
+    tests/reads.mstats \
+    tests/reads.sam \
+    tests/reads.ustats \
+    tests/simreads_1.fq \
+    tests/simreads_2.fq \
+    tests/tRex1.idx \
+    tests/tRex1_promoters.roi.bed \
+    tests/reads.counts.select

data/md5sum.txt

@@ -10,6 +10,7 @@ e832cd0a2b0e1cfa43364610663590f3  tests/reads.fmt.srt.sam
 2610d1e63613e4e092f15aa132de3a20  tests/reads.levels
 8ee3daa36fad0e196d6d86696abed3dc  tests/reads.mstats
 f224f056226aea737d1b95d7f9ab0bbf  tests/reads.sam
+928314a9be1d53771de12192813248b1  tests/reads.counts.select
 2b465b326d17ddbe9ffb2485c165803a  tests/reads.ustats
 8f3f2215bfa31e28ea3298019a342333  tests/simreads_1.fq
 76868ccd937f018e11f293a14ad60444  tests/simreads_2.fq