From 0ef74534f2c67cf2b15b9d1cf9beeb6e0d93cc48 Mon Sep 17 00:00:00 2001 From: atsuo yamada Date: Thu, 13 Apr 2017 23:27:35 +0900 Subject: [PATCH 1/2] Support to omit pileup option --- src/cljam/pileup.clj | 2 ++ test/cljam/t_pileup.clj | 3 +++ 2 files changed, 5 insertions(+) diff --git a/src/cljam/pileup.clj b/src/cljam/pileup.clj index 6bf445ea..fbb51160 100644 --- a/src/cljam/pileup.clj +++ b/src/cljam/pileup.clj @@ -15,6 +15,8 @@ {:n-threads 0}) (defn pileup + ([bam-reader rname] + (plp/pileup bam-reader rname)) ([bam-reader rname option] (pileup bam-reader rname -1 -1 option)) ([bam-reader rname start end option] diff --git a/test/cljam/t_pileup.clj b/test/cljam/t_pileup.clj index 2ab755d4..02e0816e 100644 --- a/test/cljam/t_pileup.clj +++ b/test/cljam/t_pileup.clj @@ -39,6 +39,9 @@ (plp/pileup (bam/reader test-sorted-bam-file) "ref2" nil))) (deftest about-pileup + (is (= (with-open [r (bam/reader test-sorted-bam-file)] + (plp/pileup r "ref")) + test-bam-pileup-ref)) (is (= (with-open [r (bam/reader test-sorted-bam-file)] (plp/pileup r "ref" nil)) test-bam-pileup-ref)) From 64eeb38b8fcbe71eae014a1e8c012d0902ecbae0 Mon Sep 17 00:00:00 2001 From: atsuo yamada Date: Wed, 19 Apr 2017 14:44:19 +0900 Subject: [PATCH 2/2] Refine to code expression to pileup without option --- src/cljam/pileup.clj | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/cljam/pileup.clj b/src/cljam/pileup.clj index fbb51160..a94e7f34 100644 --- a/src/cljam/pileup.clj +++ b/src/cljam/pileup.clj @@ -16,7 +16,7 @@ (defn pileup ([bam-reader rname] - (plp/pileup bam-reader rname)) + (pileup bam-reader rname {})) ([bam-reader rname option] (pileup bam-reader rname -1 -1 option)) ([bam-reader rname start end option]