[med-svn] [picard-tools] 02/02: New upstream version 2.6.0+dfsg
Andreas Tille
tille at debian.org
Sat Sep 10 08:46:25 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch upstream
in repository picard-tools.
commit 0ce17ad40614b431b9dcb6e8d07df012bf685b74
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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