gvcf2numpy_test.go

   1 package main
   2
   3 import (
   4         "bytes"
   5         "os"
   6
   7         "github.com/kshedden/gonpy"
   8         "gopkg.in/check.v1"
   9 )
  10
  11 type gvcf2numpySuite struct{}
  12
  13 var _ = check.Suite(&gvcf2numpySuite{})
  14
  15 func (s *gvcf2numpySuite) TestFastaToNumpy(c *check.C) {
  16         var stdout bytes.Buffer
  17         var cmd gvcf2numpy
  18         exited := cmd.RunCommand("gvcf2numpy", []string{"-tag-library", "testdata/tags", "-ref", "testdata/ref", "testdata/a.1.fasta"}, &bytes.Buffer{}, &stdout, os.Stderr)
  19         c.Check(exited, check.Equals, 0)
  20         npy, err := gonpy.NewReader(&stdout)
  21         c.Assert(err, check.IsNil)
  22         variants, err := npy.GetUint16()
  23         c.Assert(err, check.IsNil)
  24         for i := 0; i < 4; i += 2 {
  25                 if variants[i] == 1 {
  26                         c.Check(variants[i+1], check.Equals, uint16(2), check.Commentf("i=%d, v=%v", i, variants))
  27                 } else {
  28                         c.Check(variants[i], check.Equals, uint16(2), check.Commentf("i=%d, v=%v", i, variants))
  29                 }
  30         }
  31         for i := 4; i < 9; i += 2 {
  32                 c.Check(variants[i], check.Equals, uint16(1), check.Commentf("i=%d, v=%v", i, variants))
  33         }
  34 }
  35
  36 func sortUints(variants []uint16) {
  37         for i := 0; i < len(variants); i += 2 {
  38                 if variants[i] > variants[i+1] {
  39                         for j := 0; j < len(variants); j++ {
  40                                 variants[j], variants[j+1] = variants[j+1], variants[j]
  41                         }
  42                         return
  43                 }
  44         }
  45 }