Pull request #179: Test for empty input to ovl-cov-stats

Merge in SAT/falconc from feature/TAG-4945-empty-stats to develop

* commit 'b07290fc74d6945d5112aca54ac59bca34ec9fa2':
  Stop writing nan for ovl-cov-stats
  Test for input input to ovl-cov-stats

falconc.nimble

@@ -1,6 +1,6 @@
 # Package
 
-version       = "1.13.0"
+version       = "1.13.1"
 author        = "Zev Kronenberg"
 author        = "Christopher Dunn"
 description   = "C Utilities for bioinformatics"

src/falconcpkg/ovl_cov_stats.nim

@@ -44,6 +44,12 @@ proc collect_from_fofn*(in_fn_list: seq[string]): seq[int] =
         allCounts.add(counts)
     return allCounts
 
+proc standardDeviation(s: RunningStat): float =
+    if s.n == 0:
+        return 0.0
+    else:
+        return stats.standardDeviation(s)
+
 proc calc_stats*(counts: seq[int]): tuple[mean, stddev, median: float, min, max, n: int] =
     var rs: RunningStat
     rs.push(counts)

tests/t_ovl_cov_stats.nim

@@ -34,7 +34,7 @@ suite "ovl_cov_stats calc_stats":
     test "empty input":
         let data: seq[int] = @[]
         let results = ovl_cov_stats.calc_stats(data)
-        let expected = (mean: float(0.0), stddev: float(NaN), median: float(0.0), min: 0, max: 0, n: 0)
+        let expected = (mean: float(0.0), stddev: float(0.0), median: float(0.0), min: 0, max: 0, n: 0)
         # If this is not converted to string, tuple comparison fails for some reason.
         check $results == $expected
 
@@ -48,14 +48,14 @@ suite "ovl_cov_stats calc_stats":
 suite "ovl_cov_stats collect_from_stream":
     # This implicitly tests the count_overlaps proc.
 
-    test "empty input":
+    test "empty stream":
         let inStr = ""
         let inStream: Stream = newStringStream(inStr)
         let results = ovl_cov_stats.collect_from_stream(inStream)
         let expected: seq[int] = @[]
         check results == expected
 
-    test "empty input":
+    test "test data 1":
         let inStr = testDataCollectFromStream1
         let inStream: Stream = newStringStream(inStr)
         let results = ovl_cov_stats.collect_from_stream(inStream)

tests/t_stats.nim

@@ -3,6 +3,19 @@ import falconcpkg/stats
 import unittest
 
 
+let expected_json_on_empty = """{
+    "sum": 0,
+    "mean": 0.0,
+    "median": 0,
+    "max": 0,
+    "N100": 0,
+    "L100": 0,
+    "N90": 0,
+    "L90": 0,
+    "N50": 0,
+    "L50": 0,
+    "esize": 0.0
+}"""
 let expected_json = """{
     "sum": 120,
     "mean": 40.0,
@@ -37,3 +50,8 @@ suite "stats":
 
         check stats.to_json(st) == expected_json
         check stats.to_table(st) == expected_table
+    test "calc_stats empty":
+        let reads = newSeq[int32](0)
+        let st = stats.calc_stats(reads)
+
+        check stats.to_json(st) == expected_json_on_empty