From ce1accf4db5f9e0271f98a4dfaa0310899ced6c8 Mon Sep 17 00:00:00 2001 From: atsuo yamada Date: Fri, 21 Apr 2017 21:39:25 +0900 Subject: [PATCH] Issue #61 (2) Examine result files of `cljam pileup` in test / Remove unused old test files --- test-resources/pileup/f.pileup | 75 +++++++ test-resources/pileup/r1.pileup | 36 ++++ test-resources/pileup/r1f.pileup | 36 ++++ test-resources/pileup/r1s.pileup | 40 ++++ test-resources/pileup/r1sf.pileup | 40 ++++ test-resources/pileup/r2.pileup | 27 +++ test-resources/pileup/r2f.pileup | 27 +++ test-resources/pileup/r2s.pileup | 191 ++++++++++++++++++ test-resources/pileup/r2sf.pileup | 191 ++++++++++++++++++ test-resources/pileup/s.pileup | 85 ++++++++ test-resources/pileup/sf.pileup | 85 ++++++++ .../{t_core.pileup => pileup/test.pileup} | 46 ++--- test-resources/t_core.view | 12 -- test/cljam/t_cli.clj | 42 ++-- test/cljam/t_common.clj | 5 + 15 files changed, 879 insertions(+), 59 deletions(-) create mode 100644 test-resources/pileup/f.pileup create mode 100644 test-resources/pileup/r1.pileup create mode 100644 test-resources/pileup/r1f.pileup create mode 100644 test-resources/pileup/r1s.pileup create mode 100644 test-resources/pileup/r1sf.pileup create mode 100644 test-resources/pileup/r2.pileup create mode 100644 test-resources/pileup/r2f.pileup create mode 100644 test-resources/pileup/r2s.pileup create mode 100644 test-resources/pileup/r2sf.pileup create mode 100644 test-resources/pileup/s.pileup create mode 100644 test-resources/pileup/sf.pileup rename test-resources/{t_core.pileup => pileup/test.pileup} (66%) delete mode 100644 test-resources/t_core.view diff --git a/test-resources/pileup/f.pileup b/test-resources/pileup/f.pileup new file mode 100644 index 00000000..7f0defa3 --- /dev/null +++ b/test-resources/pileup/f.pileup @@ -0,0 +1,75 @@ +ref 7 T 1 . ~ +ref 8 T 1 . ~ +ref 9 A 3 ... ~~~ +ref 10 G 3 ... ~~~ +ref 11 A 3 ..C ~~~ +ref 12 T 3 ... ~~~ +ref 13 A 3 ... ~~~ +ref 14 A 3 .+4AGAG.+2GG. ~~~ +ref 15 G 2 .. ~~ +ref 16 A 3 ... ~~~ +ref 17 T 3 ... ~~~ +ref 18 A 3 .-1G.+2AA. ~~~ +ref 19 G 2 *. ~~ +ref 20 C 2 .. ~~ +ref 21 T 2 .. ~~ +ref 22 G 2 .> ~~ +ref 23 T 1 > ~ +ref 24 G 1 > ~ +ref 25 C 1 > ~ +ref 26 T 1 > ~ +ref 27 A 1 > ~ +ref 28 G 1 > ~ +ref 29 T 2 >. ~~ +ref 30 A 2 >. ~~ +ref 31 G 2 >. ~~ +ref 32 G 2 >. ~~ +ref 33 C 2 >. ~~ +ref 34 A 1 > ~ +ref 35 G 1 >+1C ~ +ref 36 T 1 . ~ +ref 37 C 2 .. ~~ +ref 38 A 2 .. ~~ +ref 39 G 2 .. ~~ +ref 40 C 2 .. ~~ +ref 41 G 1 . ~ +ref 42 C 1 . ~ +ref 43 C 1 . ~ +ref 44 A 1 . ~ +ref 45 T 1 . ~ +ref2 1 A 1 . ? +ref2 2 G 2 .. ?? +ref2 3 G 2 .. ?? +ref2 4 T 2 .. ?? +ref2 5 T 2 .. ?? +ref2 6 T 3 ... ??? +ref2 7 T 3 ... ??? +ref2 8 A 3 ... ??? +ref2 9 T 3 ... ??? +ref2 10 A 4 ...C ???? +ref2 11 A 4 .... ???? +ref2 12 A 5 ..... ????? +ref2 13 A 5 ..... ????? +ref2 14 C 6 ...+4AAATTTT ?????? +ref2 15 A 6 ...... ?????? +ref2 16 A 6 ...... ?????? +ref2 17 T 6 AA.... ?????? +ref2 18 T 6 ...... ?????? +ref2 19 A 6 ...... ?????? +ref2 20 A 6 ...... ?????? +ref2 21 G 5 T.... ????? +ref2 22 T 5 ..... ????? +ref2 23 C 4 .... ???? +ref2 24 T 4 .... ???? +ref2 25 A 4 .... ???? +ref2 26 C 4 .... ???? +ref2 27 A 4 .... ???? +ref2 28 G 3 ... ??? +ref2 29 A 3 ... ??? +ref2 30 G 3 ... ??? +ref2 31 C 3 ... ??? +ref2 32 A 3 ... ??? +ref2 33 A 3 ... ??? +ref2 34 C 3 ... ??? +ref2 35 T 2 .. ?? +ref2 36 A 1 . ? diff --git a/test-resources/pileup/r1.pileup b/test-resources/pileup/r1.pileup new file mode 100644 index 00000000..a3ac12de --- /dev/null +++ b/test-resources/pileup/r1.pileup @@ -0,0 +1,36 @@ +ref2 1 N 1 A ? +ref2 2 N 2 GG ?? +ref2 3 N 2 GG ?? +ref2 4 N 2 TT ?? +ref2 5 N 2 TT ?? +ref2 6 N 3 TTT ??? +ref2 7 N 3 TTT ??? +ref2 8 N 3 AAA ??? +ref2 9 N 3 TTT ??? +ref2 10 N 4 AAAC ???? +ref2 11 N 4 AAAA ???? +ref2 12 N 5 AAAAA ????? +ref2 13 N 5 AAAAA ????? +ref2 14 N 6 CCC+4AAATTTT ?????? +ref2 15 N 6 AAAAAA ?????? +ref2 16 N 6 AAAAAA ?????? +ref2 17 N 6 AATTTT ?????? +ref2 18 N 6 TTTTTT ?????? +ref2 19 N 6 AAAAAA ?????? +ref2 20 N 6 AAAAAA ?????? +ref2 21 N 5 TGGGG ????? +ref2 22 N 5 TTTTT ????? +ref2 23 N 4 CCCC ???? +ref2 24 N 4 TTTT ???? +ref2 25 N 4 AAAA ???? +ref2 26 N 4 CCCC ???? +ref2 27 N 4 AAAA ???? +ref2 28 N 3 GGG ??? +ref2 29 N 3 AAA ??? +ref2 30 N 3 GGG ??? +ref2 31 N 3 CCC ??? +ref2 32 N 3 AAA ??? +ref2 33 N 3 AAA ??? +ref2 34 N 3 CCC ??? +ref2 35 N 2 TT ?? +ref2 36 N 1 A ? diff --git a/test-resources/pileup/r1f.pileup b/test-resources/pileup/r1f.pileup new file mode 100644 index 00000000..eb40366d --- /dev/null +++ b/test-resources/pileup/r1f.pileup @@ -0,0 +1,36 @@ +ref2 1 A 1 . ? +ref2 2 G 2 .. ?? +ref2 3 G 2 .. ?? +ref2 4 T 2 .. ?? +ref2 5 T 2 .. ?? +ref2 6 T 3 ... ??? +ref2 7 T 3 ... ??? +ref2 8 A 3 ... ??? +ref2 9 T 3 ... ??? +ref2 10 A 4 ...C ???? +ref2 11 A 4 .... ???? +ref2 12 A 5 ..... ????? +ref2 13 A 5 ..... ????? +ref2 14 C 6 ...+4AAATTTT ?????? +ref2 15 A 6 ...... ?????? +ref2 16 A 6 ...... ?????? +ref2 17 T 6 AA.... ?????? +ref2 18 T 6 ...... ?????? +ref2 19 A 6 ...... ?????? +ref2 20 A 6 ...... ?????? +ref2 21 G 5 T.... ????? +ref2 22 T 5 ..... ????? +ref2 23 C 4 .... ???? +ref2 24 T 4 .... ???? +ref2 25 A 4 .... ???? +ref2 26 C 4 .... ???? +ref2 27 A 4 .... ???? +ref2 28 G 3 ... ??? +ref2 29 A 3 ... ??? +ref2 30 G 3 ... ??? +ref2 31 C 3 ... ??? +ref2 32 A 3 ... ??? +ref2 33 A 3 ... ??? +ref2 34 C 3 ... ??? +ref2 35 T 2 .. ?? +ref2 36 A 1 . ? diff --git a/test-resources/pileup/r1s.pileup b/test-resources/pileup/r1s.pileup new file mode 100644 index 00000000..5da26491 --- /dev/null +++ b/test-resources/pileup/r1s.pileup @@ -0,0 +1,40 @@ +1 +2 +2 +2 +2 +3 +3 +3 +3 +4 +4 +5 +5 +6 +6 +6 +6 +6 +6 +6 +5 +5 +4 +4 +4 +4 +4 +3 +3 +3 +3 +3 +3 +3 +2 +1 +0 +0 +0 +0 diff --git a/test-resources/pileup/r1sf.pileup b/test-resources/pileup/r1sf.pileup new file mode 100644 index 00000000..5da26491 --- /dev/null +++ b/test-resources/pileup/r1sf.pileup @@ -0,0 +1,40 @@ +1 +2 +2 +2 +2 +3 +3 +3 +3 +4 +4 +5 +5 +6 +6 +6 +6 +6 +6 +6 +5 +5 +4 +4 +4 +4 +4 +3 +3 +3 +3 +3 +3 +3 +2 +1 +0 +0 +0 +0 diff --git a/test-resources/pileup/r2.pileup b/test-resources/pileup/r2.pileup new file mode 100644 index 00000000..0cb3b304 --- /dev/null +++ b/test-resources/pileup/r2.pileup @@ -0,0 +1,27 @@ +ref2 10 N 4 AAAC ???? +ref2 11 N 4 AAAA ???? +ref2 12 N 5 AAAAA ????? +ref2 13 N 5 AAAAA ????? +ref2 14 N 6 CCC+4AAATTTT ?????? +ref2 15 N 6 AAAAAA ?????? +ref2 16 N 6 AAAAAA ?????? +ref2 17 N 6 AATTTT ?????? +ref2 18 N 6 TTTTTT ?????? +ref2 19 N 6 AAAAAA ?????? +ref2 20 N 6 AAAAAA ?????? +ref2 21 N 5 TGGGG ????? +ref2 22 N 5 TTTTT ????? +ref2 23 N 4 CCCC ???? +ref2 24 N 4 TTTT ???? +ref2 25 N 4 AAAA ???? +ref2 26 N 4 CCCC ???? +ref2 27 N 4 AAAA ???? +ref2 28 N 3 GGG ??? +ref2 29 N 3 AAA ??? +ref2 30 N 3 GGG ??? +ref2 31 N 3 CCC ??? +ref2 32 N 3 AAA ??? +ref2 33 N 3 AAA ??? +ref2 34 N 3 CCC ??? +ref2 35 N 2 TT ?? +ref2 36 N 1 A ? diff --git a/test-resources/pileup/r2f.pileup b/test-resources/pileup/r2f.pileup new file mode 100644 index 00000000..234d180c --- /dev/null +++ b/test-resources/pileup/r2f.pileup @@ -0,0 +1,27 @@ +ref2 10 A 4 ...C ???? +ref2 11 A 4 .... ???? +ref2 12 A 5 ..... ????? +ref2 13 A 5 ..... ????? +ref2 14 C 6 ...+4AAATTTT ?????? +ref2 15 A 6 ...... ?????? +ref2 16 A 6 ...... ?????? +ref2 17 T 6 AA.... ?????? +ref2 18 T 6 ...... ?????? +ref2 19 A 6 ...... ?????? +ref2 20 A 6 ...... ?????? +ref2 21 G 5 T.... ????? +ref2 22 T 5 ..... ????? +ref2 23 C 4 .... ???? +ref2 24 T 4 .... ???? +ref2 25 A 4 .... ???? +ref2 26 C 4 .... ???? +ref2 27 A 4 .... ???? +ref2 28 G 3 ... ??? +ref2 29 A 3 ... ??? +ref2 30 G 3 ... ??? +ref2 31 C 3 ... ??? +ref2 32 A 3 ... ??? +ref2 33 A 3 ... ??? +ref2 34 C 3 ... ??? +ref2 35 T 2 .. ?? +ref2 36 A 1 . ? diff --git a/test-resources/pileup/r2s.pileup b/test-resources/pileup/r2s.pileup new file mode 100644 index 00000000..1473bb3a --- /dev/null +++ b/test-resources/pileup/r2s.pileup @@ -0,0 +1,191 @@ +4 +4 +5 +5 +6 +6 +6 +6 +6 +6 +6 +5 +5 +4 +4 +4 +4 +4 +3 +3 +3 +3 +3 +3 +3 +2 +1 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 diff --git a/test-resources/pileup/r2sf.pileup b/test-resources/pileup/r2sf.pileup new file mode 100644 index 00000000..1473bb3a --- /dev/null +++ b/test-resources/pileup/r2sf.pileup @@ -0,0 +1,191 @@ +4 +4 +5 +5 +6 +6 +6 +6 +6 +6 +6 +5 +5 +4 +4 +4 +4 +4 +3 +3 +3 +3 +3 +3 +3 +2 +1 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 diff --git a/test-resources/pileup/s.pileup b/test-resources/pileup/s.pileup new file mode 100644 index 00000000..efbbfd83 --- /dev/null +++ b/test-resources/pileup/s.pileup @@ -0,0 +1,85 @@ +0 +0 +0 +0 +0 +0 +1 +1 +3 +3 +3 +3 +3 +3 +2 +3 +3 +3 +2 +2 +2 +2 +1 +1 +1 +1 +1 +1 +2 +2 +2 +2 +2 +1 +1 +1 +2 +2 +2 +2 +1 +1 +1 +1 +1 +1 +2 +2 +2 +2 +3 +3 +3 +3 +4 +4 +5 +5 +6 +6 +6 +6 +6 +6 +6 +5 +5 +4 +4 +4 +4 +4 +3 +3 +3 +3 +3 +3 +3 +2 +1 +0 +0 +0 +0 diff --git a/test-resources/pileup/sf.pileup b/test-resources/pileup/sf.pileup new file mode 100644 index 00000000..efbbfd83 --- /dev/null +++ b/test-resources/pileup/sf.pileup @@ -0,0 +1,85 @@ +0 +0 +0 +0 +0 +0 +1 +1 +3 +3 +3 +3 +3 +3 +2 +3 +3 +3 +2 +2 +2 +2 +1 +1 +1 +1 +1 +1 +2 +2 +2 +2 +2 +1 +1 +1 +2 +2 +2 +2 +1 +1 +1 +1 +1 +1 +2 +2 +2 +2 +3 +3 +3 +3 +4 +4 +5 +5 +6 +6 +6 +6 +6 +6 +6 +5 +5 +4 +4 +4 +4 +4 +3 +3 +3 +3 +3 +3 +3 +2 +1 +0 +0 +0 +0 diff --git a/test-resources/t_core.pileup b/test-resources/pileup/test.pileup similarity index 66% rename from test-resources/t_core.pileup rename to test-resources/pileup/test.pileup index ed863d5b..d42f2cc6 100644 --- a/test-resources/t_core.pileup +++ b/test-resources/pileup/test.pileup @@ -1,75 +1,75 @@ -ref 7 N 1 ^?T ~ +ref 7 N 1 T ~ ref 8 N 1 T ~ -ref 9 N 3 A^?A^?A ~~~ +ref 9 N 3 AAA ~~~ ref 10 N 3 GGG ~~~ ref 11 N 3 AAC ~~~ ref 12 N 3 TTT ~~~ ref 13 N 3 AAA ~~~ -ref 14 N 3 A+4AGAGA+2GGA$ ~~~ +ref 14 N 3 A+4AGAGA+2GGA ~~~ ref 15 N 2 GG ~~ -ref 16 N 3 AA^?A ~~~ +ref 16 N 3 AAA ~~~ ref 17 N 3 TTT ~~~ -ref 18 N 3 AA+2AA$A ~~~ +ref 18 N 3 A-1NA+2AAA ~~~ ref 19 N 2 *G ~~ ref 20 N 2 CC ~~ ref 21 N 2 TT ~~ -ref 22 N 2 G$> ~~ +ref 22 N 2 G> ~~ ref 23 N 1 > ~ ref 24 N 1 > ~ ref 25 N 1 > ~ ref 26 N 1 > ~ ref 27 N 1 > ~ ref 28 N 1 > ~ -ref 29 N 2 >^?T ~~ +ref 29 N 2 >T ~~ ref 30 N 2 >A ~~ ref 31 N 2 >G ~~ ref 32 N 2 >G ~~ -ref 33 N 2 >C$ ~~ +ref 33 N 2 >C ~~ ref 34 N 1 > ~ ref 35 N 1 >+1C ~ ref 36 N 1 T ~ -ref 37 N 2 C^?C ~~ +ref 37 N 2 CC ~~ ref 38 N 2 AA ~~ ref 39 N 2 GG ~~ -ref 40 N 2 C$C ~~ +ref 40 N 2 CC ~~ ref 41 N 1 G ~ ref 42 N 1 C ~ ref 43 N 1 C ~ ref 44 N 1 A ~ -ref 45 N 1 T$ ~ -ref2 1 N 1 ^?A ? -ref2 2 N 2 G^?G ?? +ref 45 N 1 T ~ +ref2 1 N 1 A ? +ref2 2 N 2 GG ?? ref2 3 N 2 GG ?? ref2 4 N 2 TT ?? ref2 5 N 2 TT ?? -ref2 6 N 3 TT^?T ??? +ref2 6 N 3 TTT ??? ref2 7 N 3 TTT ??? ref2 8 N 3 AAA ??? ref2 9 N 3 TTT ??? -ref2 10 N 4 AAA^?C ???? +ref2 10 N 4 AAAC ???? ref2 11 N 4 AAAA ???? -ref2 12 N 5 AAAA^?A ????? +ref2 12 N 5 AAAAA ????? ref2 13 N 5 AAAAA ????? -ref2 14 N 6 CCC+4AAATTT^?T ?????? +ref2 14 N 6 CCC+4AAATTTT ?????? ref2 15 N 6 AAAAAA ?????? ref2 16 N 6 AAAAAA ?????? ref2 17 N 6 AATTTT ?????? ref2 18 N 6 TTTTTT ?????? ref2 19 N 6 AAAAAA ?????? -ref2 20 N 6 A$AAAAA ?????? +ref2 20 N 6 AAAAAA ?????? ref2 21 N 5 TGGGG ????? -ref2 22 N 5 T$TTTT ????? +ref2 22 N 5 TTTTT ????? ref2 23 N 4 CCCC ???? ref2 24 N 4 TTTT ???? ref2 25 N 4 AAAA ???? ref2 26 N 4 CCCC ???? -ref2 27 N 4 A$AAA ???? +ref2 27 N 4 AAAA ???? ref2 28 N 3 GGG ??? ref2 29 N 3 AAA ??? ref2 30 N 3 GGG ??? ref2 31 N 3 CCC ??? ref2 32 N 3 AAA ??? ref2 33 N 3 AAA ??? -ref2 34 N 3 C$CC ??? -ref2 35 N 2 T$T ?? -ref2 36 N 1 A$ ? +ref2 34 N 3 CCC ??? +ref2 35 N 2 TT ?? +ref2 36 N 1 A ? diff --git a/test-resources/t_core.view b/test-resources/t_core.view deleted file mode 100644 index f27b9ab9..00000000 --- a/test-resources/t_core.view +++ /dev/null @@ -1,12 +0,0 @@ -r003 16 ref 29 30 6H5M * 0 0 TAGGC * -r001 163 ref 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 -r002 0 ref 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * -r003 0 ref 9 30 5H6M * 0 0 AGCTAA * -x3 0 ref2 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? -r004 0 ref 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * -r001 83 ref 37 30 9M = 7 -39 CAGCGCCAT * -x1 0 ref2 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA ???????????????????? -x2 0 ref2 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? -x4 0 ref2 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? -x6 0 ref2 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? -x5 0 ref2 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? diff --git a/test/cljam/t_cli.clj b/test/cljam/t_cli.clj index 81a90423..cc5402cd 100644 --- a/test/cljam/t_cli.clj +++ b/test/cljam/t_cli.clj @@ -92,30 +92,24 @@ :after (clean-cache!)} ;; NB: "pileup" output format may change in future (maybe) (is (not-throw? (with-out-file temp-out (cli/pileup [test-sorted-bam-file])))) - ;; (is (= (slurp temp-out) (slurp "test-resources/t_cli.pileup"))) - (are [?args] (not-throw? (with-out-file temp-out (cli/pileup ?args))) - ["-t" "1" "-s" test-sorted-bam-file] - ["-t" "1" "-f" test-fa-file test-sorted-bam-file] - ["-t" "1" "-s" "-f" test-fa-file test-sorted-bam-file] - ["-t" "1" "-r" "ref2:10-200" test-sorted-bam-file] - ["-t" "1" "-r" "ref2:10-200" "-s" test-sorted-bam-file] - ["-t" "1" "-r" "ref2:10-200" "-f" test-fa-file test-sorted-bam-file] - ["-t" "1" "-r" "ref2:10-200" "-s" "-f" test-fa-file test-sorted-bam-file] - ["-t" "1" "-r" "ref2" test-sorted-bam-file] - ["-t" "1" "-r" "ref2" "-s" test-sorted-bam-file] - ["-t" "1" "-r" "ref2" "-f" test-fa-file test-sorted-bam-file] - ["-t" "1" "-r" "ref2" "-s" "-f" test-fa-file test-sorted-bam-file] - ["-t" "4" "-s" test-sorted-bam-file] - ["-t" "4" "-f" test-fa-file test-sorted-bam-file] - ["-t" "4" "-s" "-f" test-fa-file test-sorted-bam-file] - ["-t" "4" "-r" "ref2:10-200" test-sorted-bam-file] - ["-t" "4" "-r" "ref2:10-200" "-s" test-sorted-bam-file] - ["-t" "4" "-r" "ref2:10-200" "-f" test-fa-file test-sorted-bam-file] - ["-t" "4" "-r" "ref2:10-200" "-s" "-f" test-fa-file test-sorted-bam-file] - ["-t" "4" "-r" "ref2" test-sorted-bam-file] - ["-t" "4" "-r" "ref2" "-s" test-sorted-bam-file] - ["-t" "4" "-r" "ref2" "-f" test-fa-file test-sorted-bam-file] - ["-t" "4" "-r" "ref2" "-s" "-f" test-fa-file test-sorted-bam-file]))) + (is (= (slurp temp-out) (slurp test-pileup-file))) + (let [bam-file test-sorted-bam-file] + (doseq [t ["1" "4"]] + (are [?args ?file] (= (do + (with-out-file temp-out (cli/pileup ?args)) + (slurp temp-out)) + (slurp (str test-pileup-dir ?file))) + ["-t" t "-s" bam-file] "s.pileup" + ["-t" t "-f" test-fa-file bam-file] "f.pileup" + ["-t" t "-s" "-f" test-fa-file bam-file] "sf.pileup" + ["-t" t "-r" "ref2" bam-file] "r1.pileup" + ["-t" t "-r" "ref2" "-s" bam-file] "r1s.pileup" + ["-t" t "-r" "ref2" "-f" test-fa-file bam-file] "r1f.pileup" + ["-t" t "-r" "ref2" "-s" "-f" test-fa-file bam-file] "r1sf.pileup" + ["-t" t "-r" "ref2:10-200" bam-file] "r2.pileup" + ["-t" t "-r" "ref2:10-200" "-s" bam-file] "r2s.pileup" + ["-t" t "-r" "ref2:10-200" "-f" test-fa-file bam-file] "r2f.pileup" + ["-t" t "-r" "ref2:10-200" "-s" "-f" test-fa-file bam-file] "r2sf.pileup"))))) (deftest about-faidx (with-before-after {:before (do (prepare-cache!) diff --git a/test/cljam/t_common.clj b/test/cljam/t_common.clj index 4112f0fa..ad17bfee 100644 --- a/test/cljam/t_common.clj +++ b/test/cljam/t_common.clj @@ -140,6 +140,11 @@ (def test-vcf-v4_0-file "test-resources/vcf/test-v4_0.vcf") (def test-vcf-v4_3-file "test-resources/vcf/test-v4_3.vcf") +;; ### pileup files + +(def test-pileup-file "test-resources/pileup/test.pileup") +(def test-pileup-dir "test-resources/pileup/") + (def test-sam {:header {:SQ [{:SN "ref", :LN 45} {:SN "ref2", :LN 40}]} :alignments