TST+BUG Fix CIGAR size calculation for insertions

closes #109
ngless-toolkit · Jun 7, 2019 · 31a4648 · 31a4648
1 parent 7b3e45d
commit 31a4648
Show file tree

Hide file tree

Showing 5 changed files with 17 additions and 1 deletion.
diff --git a/ChangeLog b/ChangeLog
@@ -1,5 +1,6 @@
 Version 1.0.0+
 	* Reintroduce zstd compression (after fixes upstream)
+	* Fix CIGAR interpretation (#109) occurring when I is present
 
 Version 1.0.0 2019-04-24 by luispedro
 	* Fix multiple features usage (#63)

diff --git a/NGLess/Data/Sam.hs b/NGLess/Data/Sam.hs
@@ -203,6 +203,7 @@ matchSize' includeSoft cigar
                             'M' -> n
                             '=' -> n
                             'X' -> n
+                            'I' -> n
                             'S'
                                 | includeSoft -> n
                             _ -> 0

diff --git a/Tests-Src/Tests/Select.hs b/Tests-Src/Tests/Select.hs
@@ -39,6 +39,9 @@ simulated:1:1:38:663#0	0	Ref1	1018	3	69M16S	=	1018	0	TTCGAGAAGATGGGTATCGTGGGAAAT
 complex = [here|
 SRR070372.3	16	V	7198336	21	26M3D9M3D6M6D8M2D21M	*	0	0	CCCTTATGCAGGTCTTAACACAATTCTTGTATGTTCCATCGTTCTCCAGAATGAATATCAATGATACCAA	014<<BBBBDDFFFDDDDFHHFFD?@??DBBBB5555::?=BBBBDDF@BBFHHHHHHHFFFFFD@@@@@	NM:i:14	MD:Z:26^TTT9^TTC6^TTTTTT8^AA21	AS:i:3	XS:i:0|]
 
+refinsert = [here|
+SRR6028238.2619770	417	X	1319005	0	5M1I40M54H	=	2019245	700291	TTTTCCGCTGAATATGCCCAAAGTGCAACAACGACGACCGCCGCCA	@DDDEDDDDBDDDEEECDDDDDCAACCCCBBDDDBBBBBB<@BBDB	NM:i:1	MD:Z:45	MC:Z:51M50H	AS:i:40|]
+
 case_read_one_Sam_Line = readSamLine samLineFlat @?= Right samLine
 case_encode = (BL.toStrict . BB.toLazyByteString . encodeSamLine $ samLine) @?= samLineFlat
 
@@ -48,7 +51,10 @@ case_match_identity_soft = fromRight (matchIdentity samLine) == 0.975 @? "Soft c
 case_matchSize1 = fromRight (matchSize =<< readSamLine complex) @?= (26+  9+  6+  8+  21)
                                                                    --26M3D9M3D6M6D8M2D21M
 case_matchSize2 = fromRight (matchSize =<< readSamLine simple) @?= 69
+case_matchSize3 = fromRight (matchSize =<< readSamLine refinsert) @?= 46
 
 case_cigarOK = fixCigar "9M" 9 @?= Right "9M"
 case_cigarH = fixCigar "4H5M" 9 @?= Right "4S5M"
 case_cigarH2 = fixCigar "4H5M2H" 11 @?= Right "4S5M2S"
+case_cigarH3 = fixCigar "5M1I40M54H" 46 @?= Right "5M1I40M54H"
+case_cigarH4 = fixCigar "5M1I40M54H" 100 @?= Right "5M1I40M54S"
diff --git a/tests/regression-cigar-filter/expected.result.sam b/tests/regression-cigar-filter/expected.result.sam
@@ -0,0 +1,8 @@
+@HD	VN:1.3	SO:queryname
+@SQ	SN:JPJG01000058	LN:30739
+@SQ	SN:JPJG01000046	LN:31516
+@SQ	SN:JPJG01000064	LN:32447
+@SQ	SN:JPJG01000062	LN:34508
+@SQ	SN:JPJG01000019	LN:57080
+CAU6DANXX170407:1:1305:7399:79647	321	JPJG01000058	21821	0	32S35M1I12M20S	JPJG01000019	27967	0	CGCGCATGTCGCGCCAAAAAACGATTAAAATTTATTTCGCGTCTGCGGACGCGAAAGTCTGCGACGCTGGCGCCTGTTTTCTGCCCGCAAGGGCAGAAAA	FFFFFF<FFBFFFBFFFFBFFFFFFFFFFFFFFFFFBFFFFF<FFFFFFFFFFFFFFFFFFFFFFFFFFFFBBFFFFFFBFFFFFFFFFFFFFFFBBBBB	NM:i:1	MD:Z:47	MC:Z:101M	AS:i:40
+CAU6DANXX170407:1:1305:7399:79647	161	JPJG01000019	27967	60	101M	JPJG01000062	32728	0	GGCATCGGCATCGCCGTGGAAAAGGGCTTCCAGGGCGGCGGTGACCGCTTCCGCGCGAGCGGTATCCCCTACAAGGCACTCGCCGTCATCGAAAAGGCGGA	BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<FFFFFFFFFFFFBFFFFFFBBBFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFF<	NM:i:1	MD:Z:77G23	MC:Z:15S53M32S	AS:i:96	XS:i:35
diff --git a/tests/regression-cigar-filter/select_sort.ngl b/tests/regression-cigar-filter/select_sort.ngl
@@ -7,4 +7,4 @@ mapped = select(mapped) using |mr|:
 
 mapped = samtools_sort(mapped, by={name})
 
-write(mapped, ofile='result.sam')
+write(mapped, ofile='output.result.sam')