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Fix parsing comma-separated number in region #111

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merged 1 commit into from Sep 19, 2017
Merged

Fix parsing comma-separated number in region #111

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2 changes: 1 addition & 1 deletion src/cljam/util/region.clj
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Expand Up @@ -127,7 +127,7 @@
"Parse a region string into a map."
[region-str]
(when region-str
(let [pattern #"([!-)+-<>-~][!-~]*?)(:(\d+)?(-(\d+))?)?"
(let [pattern #"([!-)+-<>-~][!-~]*?)(:([\d,]+)?(-([\d,]+))?)?"
[_ chr _ start _ end] (re-matches pattern region-str)
start' (proton/as-long start)
end' (proton/as-long end)]
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3 changes: 2 additions & 1 deletion test/cljam/util/region_test.clj
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Expand Up @@ -210,6 +210,7 @@
"chr1:1" {:chr "chr1", :start 1}
"chr1:1-" {:chr "chr1:1-"}
"chr1:1-2" {:chr "chr1", :start 1, :end 2}
"chr1:1,000-2,000" {:chr "chr1", :start 1000, :end 2000}
"chr1:-2" {:chr "chr1", :end 2}
"chr1:001-200" {:chr "chr1", :start 1, :end 200}
"chr1:100-2" {:chr "chr1", :start 100, :end 2}
Expand Down Expand Up @@ -237,6 +238,7 @@
"chr1:1" nil
"chr1:1-" nil
"chr1:1-2" {:chr "chr1", :start 1, :end 2}
"chr1:1,000-2,000" {:chr "chr1", :start 1000, :end 2000}
"chr1:-2" nil
"chr1:001-200" {:chr "chr1", :start 1, :end 200}
"chr1:100-2" nil
Expand Down Expand Up @@ -269,4 +271,3 @@
{:chr "chr1", :end 10} nil
{:start 1} nil
{:end 10} nil))