[med-svn] [picard-tools] 06/06: New upstream version 2.6.0+dfsg

Andreas Tille tille at debian.org
Sat Sep 10 08:51:31 UTC 2016 

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository picard-tools.

commit 1489b2ed92975a229125ea7dda4e561870f24b70
Author: Andreas Tille <tille at debian.org>
Date:   Sat Sep 10 10:30:19 2016 +0200

    New upstream version 2.6.0+dfsg
---
 .../25T8B25T/sams_with_4M/indicies/AAAAAAAA.sam.bak    |  2 --
 .../25T8B25T/sams_with_4M/indicies/AAAAGAAG.sam.bak    |  2 --
 .../25T8B25T/sams_with_4M/indicies/AACAATGG.sam.bak    |  6 ------
 .../25T8B25T/sams_with_4M/indicies/AACGCATT.sam.bak    |  9 ---------
 .../25T8B25T/sams_with_4M/indicies/ACAAAATT.sam.bak    |  2 --
 .../25T8B25T/sams_with_4M/indicies/ACAGGTAT.sam.bak    |  6 ------
 .../25T8B25T/sams_with_4M/indicies/ACAGTTGA.sam.bak    |  4 ----
 .../25T8B25T/sams_with_4M/indicies/ACCAGTTG.sam.bak    |  2 --
 .../25T8B25T/sams_with_4M/indicies/ACGAAATC.sam.bak    |  2 --
 .../25T8B25T/sams_with_4M/indicies/ACTAAGAC.sam.bak    |  6 ------
 .../25T8B25T/sams_with_4M/indicies/ACTGTACC.sam.bak    |  2 --
 .../25T8B25T/sams_with_4M/indicies/ACTGTATC.sam.bak    |  6 ------
 .../25T8B25T/sams_with_4M/indicies/AGAAAAGA.sam.bak    |  2 --
 .../25T8B25T/sams_with_4M/indicies/AGCATGGA.sam.bak    |  5 -----
 .../25T8B25T/sams_with_4M/indicies/AGGTAAGG.sam.bak    |  6 ------
 .../25T8B25T/sams_with_4M/indicies/AGGTCGCA.sam.bak    |  6 ------
 .../25T8B25T/sams_with_4M/indicies/ATTATCAA.sam.bak    |  7 -------
 .../25T8B25T/sams_with_4M/indicies/ATTCCTCT.sam.bak    |  6 ------
 .../25T8B25T/sams_with_4M/indicies/CAACTCTC.sam.bak    |  7 -------
 .../25T8B25T/sams_with_4M/indicies/CAATAGAC.sam.bak    |  2 --
 .../25T8B25T/sams_with_4M/indicies/CAATAGTC.sam.bak    |  9 ---------
 .../25T8B25T/sams_with_4M/indicies/CAGCGGAT.sam.bak    |  2 --
 .../25T8B25T/sams_with_4M/indicies/CAGCGGTA.sam.bak    |  7 -------
 .../25T8B25T/sams_with_4M/indicies/CCAACATT.sam.bak    |  9 ---------
 .../25T8B25T/sams_with_4M/indicies/CCAGCACC.sam.bak    |  5 -----
 .../25T8B25T/sams_with_4M/indicies/CCATGCGT.sam.bak    |  2 --
 .../25T8B25T/sams_with_4M/indicies/CGCCTTCC.sam.bak    |  4 ----
 .../25T8B25T/sams_with_4M/indicies/CGCTATGT.sam.bak    |  7 -------
 .../25T8B25T/sams_with_4M/indicies/CTAACTCG.sam.bak    |  6 ------
 .../25T8B25T/sams_with_4M/indicies/CTATGCGC.sam.bak    |  2 --
 .../25T8B25T/sams_with_4M/indicies/CTATGCGT.sam.bak    |  9 ---------
 .../25T8B25T/sams_with_4M/indicies/CTGCGGAT.sam.bak    |  5 -----
 .../25T8B25T/sams_with_4M/indicies/CTGTAATC.sam.bak    |  8 --------
 .../25T8B25T/sams_with_4M/indicies/GAAAAAAA.sam.bak    |  2 --
 .../25T8B25T/sams_with_4M/indicies/GAACGAT..sam.bak    |  2 --
 .../25T8B25T/sams_with_4M/indicies/GAAGGAAG.sam.bak    |  5 -----
 .../25T8B25T/sams_with_4M/indicies/GACCAGGA.sam.bak    |  9 ---------
 .../25T8B25T/sams_with_4M/indicies/GACCAGGC.sam.bak    |  2 --
 .../25T8B25T/sams_with_4M/indicies/GACCGTTG.sam.bak    |  6 ------
 .../25T8B25T/sams_with_4M/indicies/GACCTAAC.sam.bak    |  3 ---
 .../25T8B25T/sams_with_4M/indicies/GATATCCA.sam.bak    |  5 -----
 .../25T8B25T/sams_with_4M/indicies/GCCGTCGA.sam.bak    |  7 -------
 .../25T8B25T/sams_with_4M/indicies/GCCTAGCC.sam.bak    |  7 -------
 .../25T8B25T/sams_with_4M/indicies/GTAACATC.sam.bak    |  4 ----
 .../25T8B25T/sams_with_4M/indicies/GTCCACAG.sam.bak    |  4 ----
 .../illumina/25T8B25T/sams_with_4M/indicies/N.sam.bak  | 18 ------------------
 .../25T8B25T/sams_with_4M/indicies/TAAGCACA.sam.bak    |  4 ----
 .../25T8B25T/sams_with_4M/indicies/TACCGTCT.sam.bak    |  2 --
 .../25T8B25T/sams_with_4M/indicies/TAGCGGTA.sam.bak    |  2 --
 .../25T8B25T/sams_with_4M/indicies/TATCAGCC.sam.bak    |  2 --
 .../25T8B25T/sams_with_4M/indicies/TATCCAGG.sam.bak    |  6 ------
 .../25T8B25T/sams_with_4M/indicies/TATCCATG.sam.bak    |  2 --
 .../25T8B25T/sams_with_4M/indicies/TATCTCGG.sam.bak    |  2 --
 .../25T8B25T/sams_with_4M/indicies/TATCTGCC.sam.bak    |  9 ---------
 .../25T8B25T/sams_with_4M/indicies/TCCGTCTA.sam.bak    |  2 --
 .../25T8B25T/sams_with_4M/indicies/TCGCTAGA.sam.bak    |  7 -------
 .../25T8B25T/sams_with_4M/indicies/TCTGCAAG.sam.bak    |  3 ---
 .../25T8B25T/sams_with_4M/indicies/TGCAAGTA.sam.bak    |  4 ----
 .../25T8B25T/sams_with_4M/indicies/TGCTGCTG.sam.bak    |  6 ------
 .../25T8B25T/sams_with_4M/indicies/TGTAACTC.sam.bak    |  3 ---
 .../25T8B25T/sams_with_4M/indicies/TGTAATCA.sam.bak    |  5 -----
 .../25T8B25T/sams_with_4M/indicies/TTGTCTAT.sam.bak    |  6 ------
 62 files changed, 304 deletions(-)

diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AAAAAAAA.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AAAAAAAA.sam.bak
deleted file mode 100644
index 4882d35..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AAAAAAAA.sam.bak
+++ /dev/null
@@ -1,2 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_AAAAAAAA	LB:LN_AAAAAAAA	PL:illumina	PU:HiMom.1.AAAAAAAA	CN:BI
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AAAAGAAG.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AAAAGAAG.sam.bak
deleted file mode 100644
index 6446f79..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AAAAGAAG.sam.bak
+++ /dev/null
@@ -1,2 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_AAAAGAAG	LB:LN_AAAAGAAG	PL:illumina	PU:HiMom.1.AAAAGAAG	CN:BI
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AACAATGG.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AACAATGG.sam.bak
deleted file mode 100644
index d8ae59e..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AACAATGG.sam.bak
+++ /dev/null
@@ -1,6 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_AACAATGG	LB:LN_AACAATGG	PL:illumina	PU:HiMom.1.AACAATGG	CN:BI
-HiMom:1:1101:1138:2141	4	*	0	0	*	*	0	0	TCCG	CCCF	RG:Z:HiMom.1
-HiMom:1:1101:1206:2126	4	*	0	0	*	*	0	0	ATCT	CCCF	RG:Z:HiMom.1
-HiMom:1:2101:1077:2139	4	*	0	0	*	*	0	0	.ATT	#4=D	RG:Z:HiMom.1
-HiMom:1:2101:1112:2245	4	*	0	0	*	*	0	0	TCGT	?8?D	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AACGCATT.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AACGCATT.sam.bak
deleted file mode 100644
index 0abc311..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AACGCATT.sam.bak
+++ /dev/null
@@ -1,9 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_AACGCATT	LB:LN_AACGCATT	PL:illumina	PU:HiMom.1.AACGCATT	CN:BI
-HiMom:1:1101:1197:2200	4	*	0	0	*	*	0	0	ATAT	@@@F	RG:Z:HiMom.1
-HiMom:1:1101:1308:2153	516	*	0	0	*	*	0	0	TCTG	1?1=	RG:Z:HiMom.1
-HiMom:1:1101:1452:2132	4	*	0	0	*	*	0	0	ACAA	CCCF	RG:Z:HiMom.1
-HiMom:1:1201:1150:2161	4	*	0	0	*	*	0	0	TTCT	@C at F	RG:Z:HiMom.1
-HiMom:1:2101:1240:2197	516	*	0	0	*	*	0	0	ACTG	??##	RG:Z:HiMom.1
-HiMom:1:2101:1336:2109	4	*	0	0	*	*	0	0	AGAC	CCCF	RG:Z:HiMom.1
-HiMom:1:2101:1427:2081	4	*	0	0	*	*	0	0	CCGA	CCCF	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACAAAATT.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACAAAATT.sam.bak
deleted file mode 100644
index 3cfd422..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACAAAATT.sam.bak
+++ /dev/null
@@ -1,2 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_ACAAAATT	LB:LN_ACAAAATT	PL:illumina	PU:HiMom.1.ACAAAATT	CN:BI
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACAGGTAT.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACAGGTAT.sam.bak
deleted file mode 100644
index fe5bf02..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACAGGTAT.sam.bak
+++ /dev/null
@@ -1,6 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_ACAGGTAT	LB:LN_ACAGGTAT	PL:illumina	PU:HiMom.1.ACAGGTAT	CN:BI
-HiMom:1:1101:1236:2121	4	*	0	0	*	*	0	0	TTGC	CCCF	RG:Z:HiMom.1
-HiMom:1:1201:1341:2116	4	*	0	0	*	*	0	0	ATAA	####	RG:Z:HiMom.1
-HiMom:1:2101:1063:2206	4	*	0	0	*	*	0	0	.TGC	#1=D	RG:Z:HiMom.1
-HiMom:1:2101:1325:2083	4	*	0	0	*	*	0	0	TGTG	####	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACAGTTGA.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACAGTTGA.sam.bak
deleted file mode 100644
index f30b883..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACAGTTGA.sam.bak
+++ /dev/null
@@ -1,4 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_ACAGTTGA	LB:LN_ACAGTTGA	PL:illumina	PU:HiMom.1.ACAGTTGA	CN:BI
-HiMom:1:2101:1048:2238	4	*	0	0	*	*	0	0	.GTC	#11A	RG:Z:HiMom.1
-HiMom:1:2101:1216:2193	4	*	0	0	*	*	0	0	AGGC	@@@D	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACCAGTTG.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACCAGTTG.sam.bak
deleted file mode 100644
index 0df9571..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACCAGTTG.sam.bak
+++ /dev/null
@@ -1,2 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_ACCAGTTG	LB:LN_ACCAGTTG	PL:illumina	PU:HiMom.1.ACCAGTTG	CN:BI
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACGAAATC.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACGAAATC.sam.bak
deleted file mode 100644
index 1fbb7b4..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACGAAATC.sam.bak
+++ /dev/null
@@ -1,2 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_ACGAAATC	LB:LN_ACGAAATC	PL:illumina	PU:HiMom.1.ACGAAATC	CN:BI
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACTAAGAC.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACTAAGAC.sam.bak
deleted file mode 100644
index 5553231..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACTAAGAC.sam.bak
+++ /dev/null
@@ -1,6 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_ACTAAGAC	LB:LN_ACTAAGAC	PL:illumina	PU:HiMom.1.ACTAAGAC	CN:BI
-HiMom:1:1101:1259:2152	4	*	0	0	*	*	0	0	ATTT	CCCF	RG:Z:HiMom.1
-HiMom:1:1101:1261:2127	516	*	0	0	*	*	0	0	TTTT	CCCF	RG:Z:HiMom.1
-HiMom:1:2101:1021:2209	4	*	0	0	*	*	0	0	..GG	####	RG:Z:HiMom.1
-HiMom:1:2101:1262:2128	516	*	0	0	*	*	0	0	TCTT	####	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACTGTACC.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACTGTACC.sam.bak
deleted file mode 100644
index bcf9179..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACTGTACC.sam.bak
+++ /dev/null
@@ -1,2 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_ACTGTACC	LB:LN_ACTGTACC	PL:illumina	PU:HiMom.1.ACTGTACC	CN:BI
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACTGTATC.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACTGTATC.sam.bak
deleted file mode 100644
index 0abd96c..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACTGTATC.sam.bak
+++ /dev/null
@@ -1,6 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_ACTGTATC	LB:LN_ACTGTATC	PL:illumina	PU:HiMom.1.ACTGTATC	CN:BI
-HiMom:1:1201:1458:2109	4	*	0	0	*	*	0	0	GATA	CCCF	RG:Z:HiMom.1
-HiMom:1:2101:1105:2131	4	*	0	0	*	*	0	0	CAGC	CCCF	RG:Z:HiMom.1
-HiMom:1:2101:1349:2084	4	*	0	0	*	*	0	0	AGTC	<5;?	RG:Z:HiMom.1
-HiMom:1:2101:1365:2094	4	*	0	0	*	*	0	0	GCTC	CCCF	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AGAAAAGA.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AGAAAAGA.sam.bak
deleted file mode 100644
index d40aec2..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AGAAAAGA.sam.bak
+++ /dev/null
@@ -1,2 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_AGAAAAGA	LB:LN_AGAAAAGA	PL:illumina	PU:HiMom.1.AGAAAAGA	CN:BI
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AGCATGGA.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AGCATGGA.sam.bak
deleted file mode 100644
index 3ad5fb2..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AGCATGGA.sam.bak
+++ /dev/null
@@ -1,5 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_AGCATGGA	LB:LN_AGCATGGA	PL:illumina	PU:HiMom.1.AGCATGGA	CN:BI
-HiMom:1:1101:1406:2222	4	*	0	0	*	*	0	0	GGCT	;?@D	RG:Z:HiMom.1
-HiMom:1:1201:1291:2158	4	*	0	0	*	*	0	0	CGTG	@CCF	RG:Z:HiMom.1
-HiMom:1:2101:1370:2116	4	*	0	0	*	*	0	0	CACC	@@@D	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AGGTAAGG.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AGGTAAGG.sam.bak
deleted file mode 100644
index a49b502..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AGGTAAGG.sam.bak
+++ /dev/null
@@ -1,6 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_AGGTAAGG	LB:LN_AGGTAAGG	PL:illumina	PU:HiMom.1.AGGTAAGG	CN:BI
-HiMom:1:1101:1263:2236	516	*	0	0	*	*	0	0	AGTT	((0@	RG:Z:HiMom.1
-HiMom:1:2101:1054:2162	4	*	0	0	*	*	0	0	.GGA	#4=D	RG:Z:HiMom.1
-HiMom:1:2101:1163:2203	4	*	0	0	*	*	0	0	TTGG	@CCF	RG:Z:HiMom.1
-HiMom:1:2101:1249:2231	4	*	0	0	*	*	0	0	TCTC	@@@F	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AGGTCGCA.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AGGTCGCA.sam.bak
deleted file mode 100644
index 7938ca9..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AGGTCGCA.sam.bak
+++ /dev/null
@@ -1,6 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_AGGTCGCA	LB:LN_AGGTCGCA	PL:illumina	PU:HiMom.1.AGGTCGCA	CN:BI
-HiMom:1:1101:1150:2228	4	*	0	0	*	*	0	0	ATGG	8?=D	RG:Z:HiMom.1
-HiMom:1:1101:1491:2120	4	*	0	0	*	*	0	0	GGCC	CCCF	RG:Z:HiMom.1
-HiMom:1:1201:1190:2194	4	*	0	0	*	*	0	0	ACAA	CCCF	RG:Z:HiMom.1
-HiMom:1:2101:1188:2195	4	*	0	0	*	*	0	0	GCAC	CCCF	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ATTATCAA.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ATTATCAA.sam.bak
deleted file mode 100644
index 06af99c..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ATTATCAA.sam.bak
+++ /dev/null
@@ -1,7 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_ATTATCAA	LB:LN_ATTATCAA	PL:illumina	PU:HiMom.1.ATTATCAA	CN:BI
-HiMom:1:1101:1100:2207	4	*	0	0	*	*	0	0	AGGC	####	RG:Z:HiMom.1
-HiMom:1:1101:1157:2135	4	*	0	0	*	*	0	0	TTTA	CCCF	RG:Z:HiMom.1
-HiMom:1:1101:1269:2170	4	*	0	0	*	*	0	0	TTCC	@@<A	RG:Z:HiMom.1
-HiMom:1:1201:1018:2217	516	*	0	0	*	*	0	0	....	####	RG:Z:HiMom.1	XN:i:1
-HiMom:1:1201:1118:2198	4	*	0	0	*	*	0	0	AATA	C at CF	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ATTCCTCT.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ATTCCTCT.sam.bak
deleted file mode 100644
index ac10e3d..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ATTCCTCT.sam.bak
+++ /dev/null
@@ -1,6 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_ATTCCTCT	LB:LN_ATTCCTCT	PL:illumina	PU:HiMom.1.ATTCCTCT	CN:BI
-HiMom:1:1101:1309:2210	4	*	0	0	*	*	0	0	AGTG	@@?D	RG:Z:HiMom.1
-HiMom:1:1201:1018:2133	4	*	0	0	*	*	0	0	....	####	RG:Z:HiMom.1	XN:i:1
-HiMom:1:1201:1073:2225	4	*	0	0	*	*	0	0	CGTG	@BBD	RG:Z:HiMom.1
-HiMom:1:1201:1242:2207	4	*	0	0	*	*	0	0	ATCT	CCCF	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CAACTCTC.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CAACTCTC.sam.bak
deleted file mode 100644
index a43c57d..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CAACTCTC.sam.bak
+++ /dev/null
@@ -1,7 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_CAACTCTC	LB:LN_CAACTCTC	PL:illumina	PU:HiMom.1.CAACTCTC	CN:BI
-HiMom:1:1101:1140:2120	4	*	0	0	*	*	0	0	TTTT	@@@D	RG:Z:HiMom.1
-HiMom:1:1101:1328:2225	4	*	0	0	*	*	0	0	AGGA	####	RG:Z:HiMom.1
-HiMom:1:1201:1127:2112	516	*	0	0	*	*	0	0	TAAT	@<@?	RG:Z:HiMom.1
-HiMom:1:1201:1452:2143	4	*	0	0	*	*	0	0	TTTT	CCCF	RG:Z:HiMom.1
-HiMom:1:1201:1486:2146	516	*	0	0	*	*	0	0	TTTT	<<<@	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CAATAGAC.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CAATAGAC.sam.bak
deleted file mode 100644
index f800d53..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CAATAGAC.sam.bak
+++ /dev/null
@@ -1,2 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_CAATAGAC	LB:LN_CAATAGAC	PL:illumina	PU:HiMom.1.CAATAGAC	CN:BI
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CAATAGTC.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CAATAGTC.sam.bak
deleted file mode 100644
index d2c03cd..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CAATAGTC.sam.bak
+++ /dev/null
@@ -1,9 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_CAATAGTC	LB:LN_CAATAGTC	PL:illumina	PU:HiMom.1.CAATAGTC	CN:BI
-HiMom:1:1101:1316:2126	4	*	0	0	*	*	0	0	TCTT	CCCF	RG:Z:HiMom.1
-HiMom:1:1101:1399:2128	4	*	0	0	*	*	0	0	ACAA	CCCF	RG:Z:HiMom.1
-HiMom:1:1201:1054:2151	4	*	0	0	*	*	0	0	GTCA	CBCF	RG:Z:HiMom.1
-HiMom:1:1201:1345:2181	4	*	0	0	*	*	0	0	ATAC	CCCF	RG:Z:HiMom.1
-HiMom:1:1201:1392:2184	4	*	0	0	*	*	0	0	ATCT	@@BF	RG:Z:HiMom.1
-HiMom:1:2101:1172:2152	516	*	0	0	*	*	0	0	ATCG	####	RG:Z:HiMom.1
-HiMom:1:2101:1491:2093	4	*	0	0	*	*	0	0	AGAG	BCCD	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CAGCGGAT.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CAGCGGAT.sam.bak
deleted file mode 100644
index c9d3cfe..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CAGCGGAT.sam.bak
+++ /dev/null
@@ -1,2 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_CAGCGGAT	LB:LN_CAGCGGAT	PL:illumina	PU:HiMom.1.CAGCGGAT	CN:BI
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CAGCGGTA.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CAGCGGTA.sam.bak
deleted file mode 100644
index 516b931..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CAGCGGTA.sam.bak
+++ /dev/null
@@ -1,7 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_CAGCGGTA	LB:LN_CAGCGGTA	PL:illumina	PU:HiMom.1.CAGCGGTA	CN:BI
-HiMom:1:1101:1420:2213	4	*	0	0	*	*	0	0	TTCA	@CCF	RG:Z:HiMom.1
-HiMom:1:1201:1364:2113	4	*	0	0	*	*	0	0	TAAA	####	RG:Z:HiMom.1
-HiMom:1:2101:1072:2170	4	*	0	0	*	*	0	0	.GGG	#4=B	RG:Z:HiMom.1
-HiMom:1:2101:1123:2095	4	*	0	0	*	*	0	0	TCCG	@@@F	RG:Z:HiMom.1
-HiMom:1:2101:1151:2236	516	*	0	0	*	*	0	0	TTTG	####	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CCAACATT.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CCAACATT.sam.bak
deleted file mode 100644
index 448e66a..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CCAACATT.sam.bak
+++ /dev/null
@@ -1,9 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_CCAACATT	LB:LN_CCAACATT	PL:illumina	PU:HiMom.1.CCAACATT	CN:BI
-HiMom:1:1101:1083:2193	4	*	0	0	*	*	0	0	AGGC	19;3	RG:Z:HiMom.1
-HiMom:1:1101:1175:2197	4	*	0	0	*	*	0	0	AAGA	BC at F	RG:Z:HiMom.1
-HiMom:1:1201:1138:2227	516	*	0	0	*	*	0	0	GACA	=1=A	RG:Z:HiMom.1
-HiMom:1:1201:1260:2165	4	*	0	0	*	*	0	0	ATCT	@@@F	RG:Z:HiMom.1
-HiMom:1:1201:1281:2133	4	*	0	0	*	*	0	0	GCAA	CCCF	RG:Z:HiMom.1
-HiMom:1:1201:1331:2162	4	*	0	0	*	*	0	0	TAAT	CCCF	RG:Z:HiMom.1
-HiMom:1:2101:1186:2093	4	*	0	0	*	*	0	0	AATG	####	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CCAGCACC.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CCAGCACC.sam.bak
deleted file mode 100644
index 94b5235..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CCAGCACC.sam.bak
+++ /dev/null
@@ -1,5 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_CCAGCACC	LB:LN_CCAGCACC	PL:illumina	PU:HiMom.1.CCAGCACC	CN:BI
-HiMom:1:1101:1212:2230	4	*	0	0	*	*	0	0	TTTT	CCCF	RG:Z:HiMom.1
-HiMom:1:1201:1204:2228	4	*	0	0	*	*	0	0	TCTT	@?@F	RG:Z:HiMom.1
-HiMom:1:2101:1100:2085	4	*	0	0	*	*	0	0	ATCT	@@@D	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CCATGCGT.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CCATGCGT.sam.bak
deleted file mode 100644
index 29ae6d9..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CCATGCGT.sam.bak
+++ /dev/null
@@ -1,2 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_CCATGCGT	LB:LN_CCATGCGT	PL:illumina	PU:HiMom.1.CCATGCGT	CN:BI
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CGCCTTCC.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CGCCTTCC.sam.bak
deleted file mode 100644
index e25ff8c..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CGCCTTCC.sam.bak
+++ /dev/null
@@ -1,4 +0,0 @@
- at HD	VN:1N5	SO:queryname
- at RG	ID:HiMomN1	SM:SA_CGCCTTCC	LB:LN_CGCCTTCC	PL:illumina	PU:HiMomN1NCGCCTTCC	CN:BI
-HiMom:1:1201:1122:2227	4	*	0	0	*	*	0	0	GTCA	@@@F	RG:Z:HiMomN1
-HiMom:1:1201:1160:2109	4	*	0	0	*	*	0	0	ACAT	CCCF	RG:Z:HiMomN1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CGCTATGT.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CGCTATGT.sam.bak
deleted file mode 100644
index 310ff53..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CGCTATGT.sam.bak
+++ /dev/null
@@ -1,7 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_CGCTATGT	LB:LN_CGCTATGT	PL:illumina	PU:HiMom.1.CGCTATGT	CN:BI
-HiMom:1:1101:1291:2150	4	*	0	0	*	*	0	0	ACAA	CCCF	RG:Z:HiMom.1
-HiMom:1:1101:1314:2233	4	*	0	0	*	*	0	0	AGGA	@@<D	RG:Z:HiMom.1
-HiMom:1:1101:1441:2148	4	*	0	0	*	*	0	0	TTTT	CCCF	RG:Z:HiMom.1
-HiMom:1:1201:1043:2246	4	*	0	0	*	*	0	0	.GCA	#0;@	RG:Z:HiMom.1
-HiMom:1:1201:1134:2144	4	*	0	0	*	*	0	0	AGTG	B@?D	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTAACTCG.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTAACTCG.sam.bak
deleted file mode 100644
index bc5af8a..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTAACTCG.sam.bak
+++ /dev/null
@@ -1,6 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_CTAACTCG	LB:LN_CTAACTCG	PL:illumina	PU:HiMom.1.CTAACTCG	CN:BI
-HiMom:1:1101:1363:2138	4	*	0	0	*	*	0	0	GTTC	C@@F	RG:Z:HiMom.1
-HiMom:1:1201:1393:2143	4	*	0	0	*	*	0	0	GATA	C at CF	RG:Z:HiMom.1
-HiMom:1:2101:1273:2119	516	*	0	0	*	*	0	0	ATGA	>=><	RG:Z:HiMom.1
-HiMom:1:2101:1414:2098	4	*	0	0	*	*	0	0	TTGG	CCCF	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTATGCGC.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTATGCGC.sam.bak
deleted file mode 100644
index 2a5a21c..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTATGCGC.sam.bak
+++ /dev/null
@@ -1,2 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_CTATGCGC	LB:LN_CTATGCGC	PL:illumina	PU:HiMom.1.CTATGCGC	CN:BI
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTATGCGT.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTATGCGT.sam.bak
deleted file mode 100644
index b822db4..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTATGCGT.sam.bak
+++ /dev/null
@@ -1,9 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_CTATGCGT	LB:LN_CTATGCGT	PL:illumina	PU:HiMom.1.CTATGCGT	CN:BI
-HiMom:1:1201:1083:2121	4	*	0	0	*	*	0	0	ACAC	####	RG:Z:HiMom.1
-HiMom:1:1201:1185:2143	4	*	0	0	*	*	0	0	GCTG	@CCF	RG:Z:HiMom.1
-HiMom:1:1201:1219:2115	4	*	0	0	*	*	0	0	TGGG	???D	RG:Z:HiMom.1
-HiMom:1:1201:1472:2121	516	*	0	0	*	*	0	0	GTGT	=+=?	RG:Z:HiMom.1
-HiMom:1:2101:1013:2146	4	*	0	0	*	*	0	0	....	####	RG:Z:HiMom.1	XN:i:1
-HiMom:1:2101:1231:2208	4	*	0	0	*	*	0	0	AGCC	@@;1	RG:Z:HiMom.1
-HiMom:1:2101:1233:2133	516	*	0	0	*	*	0	0	TTTT	CCCF	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTGCGGAT.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTGCGGAT.sam.bak
deleted file mode 100644
index 57c9ab3..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTGCGGAT.sam.bak
+++ /dev/null
@@ -1,5 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_CTGCGGAT	LB:LN_CTGCGGAT	PL:illumina	PU:HiMom.1.CTGCGGAT	CN:BI
-HiMom:1:2101:1102:2221	4	*	0	0	*	*	0	0	ATAA	CCCF	RG:Z:HiMom.1
-HiMom:1:2101:1126:2082	4	*	0	0	*	*	0	0	TCTC	@C at D	RG:Z:HiMom.1
-HiMom:1:2101:1216:2172	4	*	0	0	*	*	0	0	GGAC	CCCF	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTGTAATC.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTGTAATC.sam.bak
deleted file mode 100644
index 25ea2e1..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTGTAATC.sam.bak
+++ /dev/null
@@ -1,8 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_CTGTAATC	LB:LN_CTGTAATC	PL:illumina	PU:HiMom.1.CTGTAATC	CN:BI
-HiMom:1:1101:1403:2194	4	*	0	0	*	*	0	0	ACAT	CCCF	RG:Z:HiMom.1
-HiMom:1:1201:1045:2105	516	*	0	0	*	*	0	0	.TTT	#0;@	RG:Z:HiMom.1
-HiMom:1:1201:1483:2126	516	*	0	0	*	*	0	0	GCAT	@@@D	RG:Z:HiMom.1
-HiMom:1:2101:1011:2102	4	*	0	0	*	*	0	0	....	####	RG:Z:HiMom.1	XN:i:1
-HiMom:1:2101:1245:2154	4	*	0	0	*	*	0	0	ACCA	CCCF	RG:Z:HiMom.1
-HiMom:1:2101:1386:2105	4	*	0	0	*	*	0	0	AGGA	B@@D	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GAAAAAAA.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GAAAAAAA.sam.bak
deleted file mode 100644
index 0bfb1f9..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GAAAAAAA.sam.bak
+++ /dev/null
@@ -1,2 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_GAAAAAAA	LB:LN_GAAAAAAA	PL:illumina	PU:HiMom.1.GAAAAAAA	CN:BI
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GAACGAT..sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GAACGAT..sam.bak
deleted file mode 100644
index 1636a99..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GAACGAT..sam.bak
+++ /dev/null
@@ -1,2 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_GAACGAT.	LB:LN_GAACGAT.	PL:illumina	PU:HiMom.1.GAACGAT.	CN:BI
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GAAGGAAG.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GAAGGAAG.sam.bak
deleted file mode 100644
index cd12272..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GAAGGAAG.sam.bak
+++ /dev/null
@@ -1,5 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_GAAGGAAG	LB:LN_GAAGGAAG	PL:illumina	PU:HiMom.1.GAAGGAAG	CN:BI
-HiMom:1:1101:1338:2175	4	*	0	0	*	*	0	0	GCTT	CCCF	RG:Z:HiMom.1
-HiMom:1:1201:1028:2202	4	*	0	0	*	*	0	0	..AA	####	RG:Z:HiMom.1	XN:i:1
-HiMom:1:2101:1084:2188	4	*	0	0	*	*	0	0	TACA	CCCF	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GACCAGGA.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GACCAGGA.sam.bak
deleted file mode 100644
index fbd1e80..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GACCAGGA.sam.bak
+++ /dev/null
@@ -1,9 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_GACCAGGA	LB:LN_GACCAGGA	PL:illumina	PU:HiMom.1.GACCAGGA	CN:BI
-HiMom:1:1101:1089:2172	4	*	0	0	*	*	0	0	TCCG	:<<?	RG:Z:HiMom.1
-HiMom:1:1101:1347:2149	4	*	0	0	*	*	0	0	GCTC	CCCF	RG:Z:HiMom.1
-HiMom:1:1201:1095:2146	4	*	0	0	*	*	0	0	ACTG	CCCF	RG:Z:HiMom.1
-HiMom:1:1201:1123:2161	516	*	0	0	*	*	0	0	CGTG	===A	RG:Z:HiMom.1
-HiMom:1:1201:1439:2156	4	*	0	0	*	*	0	0	GGAG	####	RG:Z:HiMom.1
-HiMom:1:2101:1207:2084	516	*	0	0	*	*	0	0	TCAC	@@@D	RG:Z:HiMom.1
-HiMom:1:2101:1312:2105	4	*	0	0	*	*	0	0	GTTG	@CCF	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GACCAGGC.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GACCAGGC.sam.bak
deleted file mode 100644
index 71b9f20..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GACCAGGC.sam.bak
+++ /dev/null
@@ -1,2 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_GACCAGGC	LB:LN_GACCAGGC	PL:illumina	PU:HiMom.1.GACCAGGC	CN:BI
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GACCGTTG.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GACCGTTG.sam.bak
deleted file mode 100644
index ddc4c9c..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GACCGTTG.sam.bak
+++ /dev/null
@@ -1,6 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_GACCGTTG	LB:LN_GACCGTTG	PL:illumina	PU:HiMom.1.GACCGTTG	CN:BI
-HiMom:1:1101:1218:2200	4	*	0	0	*	*	0	0	GCTC	####	RG:Z:HiMom.1
-HiMom:1:1101:1257:2223	4	*	0	0	*	*	0	0	TGCT	:?@D	RG:Z:HiMom.1
-HiMom:1:1201:1180:2119	4	*	0	0	*	*	0	0	GCTC	CCCF	RG:Z:HiMom.1
-HiMom:1:2101:1036:2087	4	*	0	0	*	*	0	0	.GTC	#4=D	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GACCTAAC.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GACCTAAC.sam.bak
deleted file mode 100644
index f849dd7..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GACCTAAC.sam.bak
+++ /dev/null
@@ -1,3 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_GACCTAAC	LB:LN_GACCTAAC	PL:illumina	PU:HiMom.1.GACCTAAC	CN:BI
-HiMom:1:1101:1302:2244	4	*	0	0	*	*	0	0	TGAA	CCCF	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GATATCCA.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GATATCCA.sam.bak
deleted file mode 100644
index dc7404e..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GATATCCA.sam.bak
+++ /dev/null
@@ -1,5 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_GATATCCA	LB:LN_GATATCCA	PL:illumina	PU:HiMom.1.GATATCCA	CN:BI
-HiMom:1:1101:1460:2176	4	*	0	0	*	*	0	0	AGGA	####	RG:Z:HiMom.1
-HiMom:1:2101:1031:2163	4	*	0	0	*	*	0	0	..AC	####	RG:Z:HiMom.1
-HiMom:1:2101:1226:2088	4	*	0	0	*	*	0	0	GCTC	==?B	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GCCGTCGA.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GCCGTCGA.sam.bak
deleted file mode 100644
index c7bcab6..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GCCGTCGA.sam.bak
+++ /dev/null
@@ -1,7 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_GCCGTCGA	LB:LN_GCCGTCGA	PL:illumina	PU:HiMom.1.GCCGTCGA	CN:BI
-HiMom:1:1101:1111:2148	4	*	0	0	*	*	0	0	GCGA	####	RG:Z:HiMom.1
-HiMom:1:1101:1221:2143	4	*	0	0	*	*	0	0	CAAT	@@@F	RG:Z:HiMom.1
-HiMom:1:1101:1327:2200	516	*	0	0	*	*	0	0	GTCA	@B at F	RG:Z:HiMom.1
-HiMom:1:2101:1122:2136	4	*	0	0	*	*	0	0	CTTG	???B	RG:Z:HiMom.1
-HiMom:1:2101:1459:2083	4	*	0	0	*	*	0	0	ATTT	CCCF	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GCCTAGCC.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GCCTAGCC.sam.bak
deleted file mode 100644
index 76a906a..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GCCTAGCC.sam.bak
+++ /dev/null
@@ -1,7 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_GCCTAGCC	LB:LN_GCCTAGCC	PL:illumina	PU:HiMom.1.GCCTAGCC	CN:BI
-HiMom:1:1101:1165:2239	4	*	0	0	*	*	0	0	ATGG	####	RG:Z:HiMom.1
-HiMom:1:1101:1290:2225	4	*	0	0	*	*	0	0	TCAG	C@@F	RG:Z:HiMom.1
-HiMom:1:1201:1280:2179	4	*	0	0	*	*	0	0	GAGG	@@BF	RG:Z:HiMom.1
-HiMom:1:1201:1300:2137	4	*	0	0	*	*	0	0	GCTC	@@?D	RG:Z:HiMom.1
-HiMom:1:2101:1023:2237	516	*	0	0	*	*	0	0	..TT	####	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GTAACATC.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GTAACATC.sam.bak
deleted file mode 100644
index 2456527..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GTAACATC.sam.bak
+++ /dev/null
@@ -1,4 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_GTAACATC	LB:LN_GTAACATC	PL:illumina	PU:HiMom.1.GTAACATC	CN:BI
-HiMom:1:1101:1188:2237	4	*	0	0	*	*	0	0	GCTT	CCCF	RG:Z:HiMom.1
-HiMom:1:2101:1208:2231	516	*	0	0	*	*	0	0	CTTT	CCCF	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GTCCACAG.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GTCCACAG.sam.bak
deleted file mode 100644
index da5c91f..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GTCCACAG.sam.bak
+++ /dev/null
@@ -1,4 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_GTCCACAG	LB:LN_GTCCACAG	PL:illumina	PU:HiMom.1.GTCCACAG	CN:BI
-HiMom:1:1101:1069:2159	4	*	0	0	*	*	0	0	GACG	<<<@	RG:Z:HiMom.1
-HiMom:1:1201:1486:2109	4	*	0	0	*	*	0	0	ACGT	CCCF	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/N.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/N.sam.bak
deleted file mode 100644
index bfdd2ea..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/N.sam.bak
+++ /dev/null
@@ -1,18 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_N	LB:LN_N	PL:illumina	PU:HiMom.1.N	CN:BI
-HiMom:1:1101:1031:2224	516	*	0	0	*	*	0	0	....	####	BC:Z:NNNNNNNN	RG:Z:HiMom.1	XN:i:1
-HiMom:1:1101:1039:2147	516	*	0	0	*	*	0	0	....	####	BC:Z:NNNNNNNN	RG:Z:HiMom.1	XN:i:1
-HiMom:1:1101:1046:2175	516	*	0	0	*	*	0	0	..GG	####	BC:Z:NNNNNNNN	RG:Z:HiMom.1
-HiMom:1:1101:1047:2122	516	*	0	0	*	*	0	0	..TC	####	BC:Z:NNNANNNN	RG:Z:HiMom.1
-HiMom:1:1101:1048:2197	516	*	0	0	*	*	0	0	..GT	####	BC:Z:NNNCNNNN	RG:Z:HiMom.1
-HiMom:1:1101:1065:2193	4	*	0	0	*	*	0	0	.CTT	####	BC:Z:GAACGATN	RG:Z:HiMom.1
-HiMom:1:1101:1162:2207	516	*	0	0	*	*	0	0	TAAA	####	BC:Z:ACAAAATT	RG:Z:HiMom.1
-HiMom:1:1201:1159:2179	516	*	0	0	*	*	0	0	TTTT	===A	BC:Z:AAAAAAAA	RG:Z:HiMom.1
-HiMom:1:1201:1414:2174	516	*	0	0	*	*	0	0	TTTT	@;@1	BC:Z:AGAAAAGA	RG:Z:HiMom.1
-HiMom:1:2101:1040:2208	516	*	0	0	*	*	0	0	.CTG	####	BC:Z:ACGAAATC	RG:Z:HiMom.1
-HiMom:1:2101:1059:2083	4	*	0	0	*	*	0	0	.GAA	#1=B	BC:Z:TACCGTCT	RG:Z:HiMom.1
-HiMom:1:2101:1143:2137	4	*	0	0	*	*	0	0	GCTC	@@@D	BC:Z:TCCGTCTA	RG:Z:HiMom.1
-HiMom:1:2101:1151:2182	516	*	0	0	*	*	0	0	TTTT	9<<?	BC:Z:GAAAAAAA	RG:Z:HiMom.1
-HiMom:1:2101:1215:2110	4	*	0	0	*	*	0	0	ATCT	####	BC:Z:AAAAGAAG	RG:Z:HiMom.1
-HiMom:1:2101:1285:2105	516	*	0	0	*	*	0	0	TGTC	####	BC:Z:TATCTCGG	RG:Z:HiMom.1
-HiMom:1:2101:1450:2134	4	*	0	0	*	*	0	0	ACAA	CC at F	BC:Z:ACCAGTTG	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TAAGCACA.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TAAGCACA.sam.bak
deleted file mode 100644
index 436fa57..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TAAGCACA.sam.bak
+++ /dev/null
@@ -1,4 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_TAAGCACA	LB:LN_TAAGCACA	PL:illumina	PU:HiMom.1.TAAGCACA	CN:BI
-HiMom:1:1201:1064:2239	4	*	0	0	*	*	0	0	GGGA	8?@:	RG:Z:HiMom.1
-HiMom:1:2101:1258:2092	4	*	0	0	*	*	0	0	TTAG	####	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TACCGTCT.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TACCGTCT.sam.bak
deleted file mode 100644
index 04cf526..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TACCGTCT.sam.bak
+++ /dev/null
@@ -1,2 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_TACCGTCT	LB:LN_TACCGTCT	PL:illumina	PU:HiMom.1.TACCGTCT	CN:BI
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TAGCGGTA.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TAGCGGTA.sam.bak
deleted file mode 100644
index 3455237..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TAGCGGTA.sam.bak
+++ /dev/null
@@ -1,2 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_TAGCGGTA	LB:LN_TAGCGGTA	PL:illumina	PU:HiMom.1.TAGCGGTA	CN:BI
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TATCAGCC.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TATCAGCC.sam.bak
deleted file mode 100644
index 5f7c0e3..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TATCAGCC.sam.bak
+++ /dev/null
@@ -1,2 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_TATCAGCC	LB:LN_TATCAGCC	PL:illumina	PU:HiMom.1.TATCAGCC	CN:BI
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TATCCAGG.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TATCCAGG.sam.bak
deleted file mode 100644
index d5753c0..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TATCCAGG.sam.bak
+++ /dev/null
@@ -1,6 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_TATCCAGG	LB:LN_TATCCAGG	PL:illumina	PU:HiMom.1.TATCCAGG	CN:BI
-HiMom:1:1101:1071:2233	4	*	0	0	*	*	0	0	GTTT	<<<@	RG:Z:HiMom.1
-HiMom:1:1201:1140:2125	4	*	0	0	*	*	0	0	TTCA	CC at F	RG:Z:HiMom.1
-HiMom:1:1201:1236:2187	4	*	0	0	*	*	0	0	CTCC	CCCF	RG:Z:HiMom.1
-HiMom:1:2101:1133:2239	4	*	0	0	*	*	0	0	AGCT	?@?D	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TATCCATG.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TATCCATG.sam.bak
deleted file mode 100644
index a5373e3..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TATCCATG.sam.bak
+++ /dev/null
@@ -1,2 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_TATCCATG	LB:LN_TATCCATG	PL:illumina	PU:HiMom.1.TATCCATG	CN:BI
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TATCTCGG.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TATCTCGG.sam.bak
deleted file mode 100644
index 04096c5..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TATCTCGG.sam.bak
+++ /dev/null
@@ -1,2 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_TATCTCGG	LB:LN_TATCTCGG	PL:illumina	PU:HiMom.1.TATCTCGG	CN:BI
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TATCTGCC.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TATCTGCC.sam.bak
deleted file mode 100644
index b66efde..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TATCTGCC.sam.bak
+++ /dev/null
@@ -1,9 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_TATCTGCC	LB:LN_TATCTGCC	PL:illumina	PU:HiMom.1.TATCTGCC	CN:BI
-HiMom:1:1101:1267:2209	4	*	0	0	*	*	0	0	GGCA	=;?D	RG:Z:HiMom.1
-HiMom:1:1101:1353:2226	4	*	0	0	*	*	0	0	GTGC	BBBF	RG:Z:HiMom.1
-HiMom:1:1101:1435:2194	4	*	0	0	*	*	0	0	TTTT	CCCF	RG:Z:HiMom.1
-HiMom:1:1201:1084:2204	4	*	0	0	*	*	0	0	TGGC	CCCF	RG:Z:HiMom.1
-HiMom:1:1201:1142:2242	4	*	0	0	*	*	0	0	GTAA	?=?D	RG:Z:HiMom.1
-HiMom:1:1201:1187:2100	4	*	0	0	*	*	0	0	AAAA	=<=;	RG:Z:HiMom.1	XN:i:1
-HiMom:1:1201:1392:2109	4	*	0	0	*	*	0	0	GTCA	BBCF	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TCCGTCTA.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TCCGTCTA.sam.bak
deleted file mode 100644
index 8f5dbc6..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TCCGTCTA.sam.bak
+++ /dev/null
@@ -1,2 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_TCCGTCTA	LB:LN_TCCGTCTA	PL:illumina	PU:HiMom.1.TCCGTCTA	CN:BI
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TCGCTAGA.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TCGCTAGA.sam.bak
deleted file mode 100644
index 9918fb0..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TCGCTAGA.sam.bak
+++ /dev/null
@@ -1,7 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_TCGCTAGA	LB:LN_TCGCTAGA	PL:illumina	PU:HiMom.1.TCGCTAGA	CN:BI
-HiMom:1:1101:1143:2192	4	*	0	0	*	*	0	0	CGAC	CCCF	RG:Z:HiMom.1
-HiMom:1:1101:1479:2221	4	*	0	0	*	*	0	0	GGGG	@CCF	RG:Z:HiMom.1
-HiMom:1:1201:1312:2112	4	*	0	0	*	*	0	0	ATTT	CCCF	RG:Z:HiMom.1
-HiMom:1:1201:1416:2128	4	*	0	0	*	*	0	0	TTGG	@@@D	RG:Z:HiMom.1
-HiMom:1:2101:1064:2242	4	*	0	0	*	*	0	0	.GGA	####	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TCTGCAAG.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TCTGCAAG.sam.bak
deleted file mode 100644
index 2c2caf0..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TCTGCAAG.sam.bak
+++ /dev/null
@@ -1,3 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_TCTGCAAG	LB:LN_TCTGCAAG	PL:illumina	PU:HiMom.1.TCTGCAAG	CN:BI
-HiMom:1:1201:1042:2174	4	*	0	0	*	*	0	0	.TCA	#0;@	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TGCAAGTA.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TGCAAGTA.sam.bak
deleted file mode 100644
index c8e5e0b..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TGCAAGTA.sam.bak
+++ /dev/null
@@ -1,4 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_TGCAAGTA	LB:LN_TGCAAGTA	PL:illumina	PU:HiMom.1.TGCAAGTA	CN:BI
-HiMom:1:1101:1242:2170	4	*	0	0	*	*	0	0	GGAA	@@@D	RG:Z:HiMom.1
-HiMom:1:2101:1163:2222	4	*	0	0	*	*	0	0	GAGC	@@@D	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TGCTGCTG.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TGCTGCTG.sam.bak
deleted file mode 100644
index 077ddf5..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TGCTGCTG.sam.bak
+++ /dev/null
@@ -1,6 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_TGCTGCTG	LB:LN_TGCTGCTG	PL:illumina	PU:HiMom.1.TGCTGCTG	CN:BI
-HiMom:1:1101:1084:2136	4	*	0	0	*	*	0	0	TTTC	<<<@	RG:Z:HiMom.1
-HiMom:1:1201:1285:2100	4	*	0	0	*	*	0	0	GATC	@@@D	RG:Z:HiMom.1
-HiMom:1:2101:1162:2139	4	*	0	0	*	*	0	0	ATCG	BCCF	RG:Z:HiMom.1
-HiMom:1:2101:1195:2150	4	*	0	0	*	*	0	0	AATT	CCCF	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TGTAACTC.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TGTAACTC.sam.bak
deleted file mode 100644
index 9034a76..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TGTAACTC.sam.bak
+++ /dev/null
@@ -1,3 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_TGTAACTC	LB:LN_TGTAACTC	PL:illumina	PU:HiMom.1.TGTAACTC	CN:BI
-HiMom:1:1201:1421:2154	4	*	0	0	*	*	0	0	TGTG	BC at D	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TGTAATCA.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TGTAATCA.sam.bak
deleted file mode 100644
index 8880ffa..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TGTAATCA.sam.bak
+++ /dev/null
@@ -1,5 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_TGTAATCA	LB:LN_TGTAATCA	PL:illumina	PU:HiMom.1.TGTAATCA	CN:BI
-HiMom:1:1101:1419:2119	4	*	0	0	*	*	0	0	ACTT	####	RG:Z:HiMom.1
-HiMom:1:1201:1208:2132	4	*	0	0	*	*	0	0	CTGT	@@CD	RG:Z:HiMom.1
-HiMom:1:1201:1344:2147	4	*	0	0	*	*	0	0	ACGA	@<??	RG:Z:HiMom.1
diff --git a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TTGTCTAT.sam.bak b/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TTGTCTAT.sam.bak
deleted file mode 100644
index fbf1f1b..0000000
--- a/testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TTGTCTAT.sam.bak
+++ /dev/null
@@ -1,6 +0,0 @@
- at HD	VN:1.5	SO:queryname
- at RG	ID:HiMom.1	SM:SA_TTGTCTAT	LB:LN_TTGTCTAT	PL:illumina	PU:HiMom.1.TTGTCTAT	CN:BI
-HiMom:1:1101:1219:2164	4	*	0	0	*	*	0	0	ATCT	CCCF	RG:Z:HiMom.1
-HiMom:1:1201:1103:2184	4	*	0	0	*	*	0	0	AGAA	B at BF	RG:Z:HiMom.1
-HiMom:1:1201:1107:2109	4	*	0	0	*	*	0	0	ACAA	CCCF	RG:Z:HiMom.1
-HiMom:1:1201:1252:2141	4	*	0	0	*	*	0	0	AGTT	BCBF	RG:Z:HiMom.1

-- 
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