# HG changeset patch
# User iuc
# Date 1430324734 14400
# Node ID fd11d2328ca80a1c4c668f3641769d5a3189197a
# Parent 8a515186854991b06524ec9dc9619590cadc6176
Uploaded
diff -r 8a5151868549 -r fd11d2328ca8 macros.xml
--- a/macros.xml Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,33 +0,0 @@
-
-
-
-
- seqtk
-
-
-
- 1.0-r75-dirty
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- `_, developed by Heng Li at the Broad Institute
- ]]>
-
-
diff -r 8a5151868549 -r fd11d2328ca8 seqtk_comp.xml
--- a/seqtk_comp.xml Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,52 +0,0 @@
-
-
- get the nucleotide composition of FASTA/Q
-
- macros.xml
-
-
-
- $default]]>
-
-
-
-
-
-
-
-
-
-
-
-
-
- test0
- ACTGACTGAA
- >ambig_ref
- ACGTCGTGTTVHDBN
-
-The seqtk tool will report:
-
-::
-
- #chr length #A #C #G #T #2 #3 #4 #CpG #tv #ts #CpG-ts
- test0 11 4 2 2 2 0 0 1 0 0 0 0
- ambig_ref 15 1 2 3 4 0 4 1 4 0 0 0
-
-
-@ATTRIBUTION@
-]]>
-
diff -r 8a5151868549 -r fd11d2328ca8 seqtk_cutN.xml
--- a/seqtk_cutN.xml Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,52 +0,0 @@
-
-
- cut sequence at long N
-
- macros.xml
-
-
-
- $default]]>
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- test
- AACTGATCGATCGATCGNNNNNNNNNNNACATG
-
-This will be split into the component sequences without the ambiguity.
-
-::
-
- >test:1-17
- AACTGATCGATCGATCG
- >test:29-33
- ACATG
-
-
-@ATTRIBUTION@
- ]]>
-
diff -r 8a5151868549 -r fd11d2328ca8 seqtk_dropse.xml
--- a/seqtk_dropse.xml Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,76 +0,0 @@
-
-
- drop unpaired from interleaved Paired End FASTA/Q
-
- macros.xml
-
-
-
- $default]]>
-
-
-
-
-
-
-
-
-
-
-
-
- >F
- @test-6/2
- TGCGAAGACC
- +
- >2?A?A@@7?
- @test-4/1
- CTTGACGCTG
- +
- I@>3EFCG@C
- @test-2/1
- AGACCAAAAT
- +
- ??><6E?IFC
- @test-2/2
- CTGGCGAATT
- +
- ?=?*?A?@
-
-This tool will remove the offending reads (test-4/1), leaving just the paired data.
-
-::
-
- @test-6/1
- AGCTTGACGC
- +
- ?.HCF@C>>F
- @test-6/2
- TGCGAAGACC
- +
- >2?A?A@@7?
- @test-2/1
- AGACCAAAAT
- +
- ??><6E?IFC
- @test-2/2
- CTGGCGAATT
- +
- ?=?*?A?@
-
-
-@ATTRIBUTION@
- ]]>
-
diff -r 8a5151868549 -r fd11d2328ca8 seqtk_fqchk.xml
--- a/seqtk_fqchk.xml Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,58 +0,0 @@
-
-
- fastq QC (base/quality summary)
-
- macros.xml
-
-
-
- $default]]>
-
-
-
-
-
-
-
-
-
-
-
-
-
- >>>>>CCCCCCC65
-
-each based is examined individually and information reported:
-
-::
-
- #min_len: 60; max_len: 60; avg_len: 60.00; 15 distinct quality values
- #POS #bases %A %C %G %T %N avgQ errQ %low %high
- #ALL 60 31.7 16.7 18.3 33.3 0.0 15.1 8.7 66.7 33.3
- 1 1 0.0 0.0 100.0 0.0 0.0 0.0 3.0 100.0 0.0
- 2 1 100.0 0.0 0.0 0.0 0.0 6.0 6.0 100.0 0.0
- 3 1 0.0 0.0 0.0 100.0 0.0 6.0 6.0 100.0 0.0
- 4 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0
- 5 1 0.0 0.0 0.0 100.0 0.0 7.0 7.0 100.0 0.0
- 6 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0
- 7 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0
- 8 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0
- 9 1 0.0 0.0 100.0 0.0 0.0 9.0 9.0 100.0 0.0
- 10 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0
-
-@ATTRIBUTION@
-]]>
-
diff -r 8a5151868549 -r fd11d2328ca8 seqtk_hety.xml
--- a/seqtk_hety.xml Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,73 +0,0 @@
-
-
- regional heterozygosity
-
- macros.xml
-
-
-
- $default]]>
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- het_region
- ACTTTACATCGAGCMMMMMMMACAGTACTG
-
-As can be seen in the following output:
-
-::
-
- #chr start end A B num_het
- het_region 0 8 0.00 8 0
- het_region 8 9 0.00 8 0
- het_region 9 10 0.00 8 0
- het_region 10 11 0.00 8 0
- het_region 11 12 0.00 8 0
- het_region 12 13 0.00 8 0
- het_region 13 14 0.00 8 0
- het_region 14 15 1.00 8 1
- het_region 15 16 2.00 8 2
- het_region 16 17 3.00 8 3
- het_region 17 18 4.00 8 4
- het_region 18 19 5.00 8 5
- het_region 19 20 6.00 8 6
- het_region 20 21 7.00 8 7
- het_region 21 22 7.00 8 7
- het_region 22 23 6.00 8 6
- het_region 23 24 5.00 8 5
- het_region 24 25 4.00 8 4
- het_region 25 26 3.00 8 3
- het_region 26 27 2.00 8 2
- het_region 27 28 1.00 8 1
- het_region 28 29 0.00 8 0
- het_region 29 30 0.00 1 0
-
-If you know what A and B are measures of, please `submit an issue `__ and it will be corrected
-
-@ATTRIBUTION@
-]]>
-
diff -r 8a5151868549 -r fd11d2328ca8 seqtk_listhet.xml
--- a/seqtk_listhet.xml Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,47 +0,0 @@
-
-
- extract the position of each het
-
- macros.xml
-
-
-
- $default]]>
-
-
-
-
-
-
-
-
-
-
-
-
- ambig
- ACGTMRWSYKVHDBN
-
-The seqtk suite recognises MRWSYK:
-
-::
-
- #chr position base
- ambig 5 M
- ambig 6 R
- ambig 7 W
- ambig 8 S
- ambig 9 Y
- ambig 10 K
-
-
-@ATTRIBUTION@
-]]>
-
diff -r 8a5151868549 -r fd11d2328ca8 seqtk_mergefa.xml
--- a/seqtk_mergefa.xml Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,68 +0,0 @@
-
-
- merge two FASTA/Q files
-
- macros.xml
-
-
-
- $default]]>
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- test0
- ACTGACTGAAA
-
- # seq2.fa
- >test0
- ACTGAMTGCGN
-
-In the following the `-m` option has been set to highlight seqtk-mergefa's features.
-
-::
-
- >test0
- ACTGACTGxxa
-
-@ATTRIBUTION@
-]]>
-
diff -r 8a5151868549 -r fd11d2328ca8 seqtk_mergepe.xml
--- a/seqtk_mergepe.xml Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,93 +0,0 @@
-
-
- interleave two unpaired FASTA/Q files for a paired-end file
-
- macros.xml
-
-
-
- $default]]>
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- >F
-
- # r2.fq
- @test-6/2
- TGCGAAGACC
- +
- >2?A?A@@7?
-
-will produce the following paired file:
-
-::
-
- @test-6/1
- AGCTTGACGC
- +
- ?.HCF@C>>F
- @test-6/2
- TGCGAAGACC
- +
- >2?A?A@@7?
-
-While this may not have been an illuminating example, it is important to note
-that this tool will properly interleave data. For example if you have the ids:
-
-::
-
- @r-1/1
- @r-2/1
- @r-3/1
- @r-4/1
-
-and
-
-::
-
- @r-1/2
- @r-2/2
- @r-3/2
- @r-4/2
-
-These will be interleaved as
-
-::
-
- @r-1/1
- @r-1/2
- @r-2/1
- @r-2/2
- @r-3/1
- @r-3/2
- @r-4/1
- @r-4/2
-
-@ATTRIBUTION@
-]]>
-
diff -r 8a5151868549 -r fd11d2328ca8 seqtk_mutfa.xml
--- a/seqtk_mutfa.xml Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,51 +0,0 @@
-
-
- point mutate FASTA at specified positions
-
- macros.xml
-
-
-
- $default]]>
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- test0
- ACTGACTGAA
-
- # Input SNP file
- test0 1 . G
- test0 4 . A
-
-This will effect the desired mutations in the output file
-
-::
-
- # Output result
- >test0
- GCTAACTGAA
-
-@ATTRIBUTION@
-]]>
-
diff -r 8a5151868549 -r fd11d2328ca8 seqtk_randbase.xml
--- a/seqtk_randbase.xml Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,45 +0,0 @@
-
-
- choose a random base from hets
-
- macros.xml
-
-
-
- $default]]>
-
-
-
-
-
-
-
-
-
-
-
-
- ambig
- ACGTMRWSYK
-
-results in
-
-::
-
- # Output result
- >ambig
- ACGTCGTGTT
-
-@ATTRIBUTION@
-]]>
-
diff -r 8a5151868549 -r fd11d2328ca8 seqtk_sample.xml
--- a/seqtk_sample.xml Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-
-
- random subsample of fasta or fastq sequences
-
- macros.xml
-
-
-
- $default]]>
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- `__.
-
-The subsample size can be a decimal fraction <=1, where 1 implies 100% of the reads should be used. If a number >1 is provided, that many reads will be taken from the dataset.
-
-@ATTRIBUTION@
-]]>
-
diff -r 8a5151868549 -r fd11d2328ca8 seqtk_seq.xml
--- a/seqtk_seq.xml Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,76 +0,0 @@
-
-
- common transformation of FASTA/Q
-
- macros.xml
-
-
-
- $default]]>
-
-
-
-
-
-
-
-
-
-
-
-
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-
-
diff -r 8a5151868549 -r fd11d2328ca8 seqtk_subseq.xml
--- a/seqtk_subseq.xml Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,83 +0,0 @@
-
-
- extract subsequences from FASTA/Q files
-
- macros.xml
-
-
-
- $default]]>
-
-
-
-
-
-
-
-
-
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-
-
-
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-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- seq1
- ACGTMRWSYK
- >seq2
- RWSYKACGTM
-
-results in
-
-::
-
- # Output result
- >seq1
- ACGTMRWSYK
-
-@ATTRIBUTION@
-]]>
-
diff -r 8a5151868549 -r fd11d2328ca8 seqtk_trimfq.xml
--- a/seqtk_trimfq.xml Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,62 +0,0 @@
-
-
- trim FASTQ using the Phred algorithm
-
- macros.xml
-
-
-
- $default]]>
-
-
-
-
-
-
-
-
-
-
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-
diff -r 8a5151868549 -r fd11d2328ca8 test-data/paired_dat.fq
--- a/test-data/paired_dat.fq Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
-@test-6/1
-AGCTTGACGC
-+
-?.HCF@C>>F
-@test-6/2
-TGCGAAGACC
-+
->2?A?A@@7?
-@test-4/1
-CTTGACGCTG
-+
-I@>3EFCG@C
-@test-4/2
-TGCGAAGACC
-+
-A?A@@B@<6E?IFC
-@test-2/2
-CTGGCGAATT
-+
-?=?*?A?@
diff -r 8a5151868549 -r fd11d2328ca8 test-data/paired_dat1.fq
--- a/test-data/paired_dat1.fq Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-@test-6/1
-AGCTTGACGC
-+
-?.HCF@C>>F
-@test-4/1
-CTTGACGCTG
-+
-I@>3EFCG@C
-@test-2/1
-AGACCAAAAT
-+
-??><6E?IFC
diff -r 8a5151868549 -r fd11d2328ca8 test-data/paired_dat2.fq
--- a/test-data/paired_dat2.fq Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-@test-6/2
-TGCGAAGACC
-+
->2?A?A@@7?
-@test-4/2
-TGCGAAGACC
-+
-A?A@@B@test0
-ACTGACTGAA
->ambig_ref
-ACGTCGTGTTVHDBN
-
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_comp.out
--- a/test-data/seqtk_comp.out Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-#chr length #A #C #G #T #2 #3 #4 #CpG #tv #ts #CpG-ts
-test0 10 4 2 2 2 0 0 0 0 0 0 0
-ambig_ref 15 1 2 3 4 0 4 1 4 0 0 0
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_cutn.fa
--- a/test-data/seqtk_cutn.fa Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
->test
-AACTGATCGATCGATCGNNNNNNNNNNNACATG
-
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_cutn.out
--- a/test-data/seqtk_cutn.out Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
->test:1-17
-AACTGATCGATCGATCG
->test:29-33
-ACATG
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_dropse.fq
--- a/test-data/seqtk_dropse.fq Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-@test-6/1
-AGCTTGACGC
-+
-?.HCF@C>>F
-@test-6/2
-TGCGAAGACC
-+
->2?A?A@@7?
-@test-4/2
-TGCGAAGACC
-+
-A?A@@B@<6E?IFC
-@test-2/2
-CTGGCGAATT
-+
-?=?*?A?@
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_dropse.out
--- a/test-data/seqtk_dropse.out Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-@test-6/1
-AGCTTGACGC
-+
-?.HCF@C>>F
-@test-6/2
-TGCGAAGACC
-+
->2?A?A@@7?
-@test-2/1
-AGACCAAAAT
-+
-??><6E?IFC
-@test-2/2
-CTGGCGAATT
-+
-?=?*?A?@
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_fqchk.fq
--- a/test-data/seqtk_fqchk.fq Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-@SEQ_ID1
-GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
-+
-!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_fqchk.out
--- a/test-data/seqtk_fqchk.out Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,63 +0,0 @@
-#min_len: 60; max_len: 60; avg_len: 60.00; 15 distinct quality values
-#POS #bases %A %C %G %T %N avgQ errQ %low %high
-#ALL 60 31.7 16.7 18.3 33.3 0.0 15.1 8.7 66.7 33.3
-1 1 0.0 0.0 100.0 0.0 0.0 0.0 3.0 100.0 0.0
-2 1 100.0 0.0 0.0 0.0 0.0 6.0 6.0 100.0 0.0
-3 1 0.0 0.0 0.0 100.0 0.0 6.0 6.0 100.0 0.0
-4 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0
-5 1 0.0 0.0 0.0 100.0 0.0 7.0 7.0 100.0 0.0
-6 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0
-7 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0
-8 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0
-9 1 0.0 0.0 100.0 0.0 0.0 9.0 9.0 100.0 0.0
-10 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0
-11 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0
-12 1 0.0 100.0 0.0 0.0 0.0 10.0 10.0 100.0 0.0
-13 1 100.0 0.0 0.0 0.0 0.0 8.0 8.0 100.0 0.0
-14 1 100.0 0.0 0.0 0.0 0.0 8.0 8.0 100.0 0.0
-15 1 100.0 0.0 0.0 0.0 0.0 4.0 4.0 100.0 0.0
-16 1 0.0 0.0 100.0 0.0 0.0 4.0 4.0 100.0 0.0
-17 1 0.0 100.0 0.0 0.0 0.0 4.0 4.0 100.0 0.0
-18 1 100.0 0.0 0.0 0.0 0.0 10.0 10.0 100.0 0.0
-19 1 0.0 0.0 100.0 0.0 0.0 10.0 10.0 100.0 0.0
-20 1 0.0 0.0 0.0 100.0 0.0 8.0 8.0 100.0 0.0
-21 1 100.0 0.0 0.0 0.0 0.0 7.0 7.0 100.0 0.0
-22 1 0.0 0.0 0.0 100.0 0.0 4.0 4.0 100.0 0.0
-23 1 0.0 100.0 0.0 0.0 0.0 4.0 4.0 100.0 0.0
-24 1 0.0 0.0 100.0 0.0 0.0 4.0 4.0 100.0 0.0
-25 1 100.0 0.0 0.0 0.0 0.0 4.0 4.0 100.0 0.0
-26 1 0.0 0.0 0.0 100.0 0.0 8.0 8.0 100.0 0.0
-27 1 0.0 100.0 0.0 0.0 0.0 13.0 13.0 100.0 0.0
-28 1 100.0 0.0 0.0 0.0 0.0 16.0 16.0 100.0 0.0
-29 1 100.0 0.0 0.0 0.0 0.0 9.0 9.0 100.0 0.0
-30 1 100.0 0.0 0.0 0.0 0.0 9.0 9.0 100.0 0.0
-31 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0
-32 1 100.0 0.0 0.0 0.0 0.0 12.0 12.0 100.0 0.0
-33 1 0.0 0.0 100.0 0.0 0.0 10.0 10.0 100.0 0.0
-34 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0
-35 1 100.0 0.0 0.0 0.0 0.0 6.0 6.0 100.0 0.0
-36 1 100.0 0.0 0.0 0.0 0.0 6.0 6.0 100.0 0.0
-37 1 100.0 0.0 0.0 0.0 0.0 8.0 8.0 100.0 0.0
-38 1 0.0 0.0 0.0 100.0 0.0 8.0 8.0 100.0 0.0
-39 1 0.0 100.0 0.0 0.0 0.0 9.0 9.0 100.0 0.0
-40 1 0.0 100.0 0.0 0.0 0.0 9.0 9.0 100.0 0.0
-41 1 100.0 0.0 0.0 0.0 0.0 20.0 20.0 0.0 100.0
-42 1 0.0 0.0 0.0 100.0 0.0 20.0 20.0 0.0 100.0
-43 1 0.0 0.0 0.0 100.0 0.0 34.0 34.0 0.0 100.0
-44 1 0.0 0.0 0.0 100.0 0.0 34.0 34.0 0.0 100.0
-45 1 0.0 0.0 100.0 0.0 0.0 37.0 37.0 0.0 100.0
-46 1 0.0 0.0 0.0 100.0 0.0 29.0 29.0 0.0 100.0
-47 1 0.0 0.0 0.0 100.0 0.0 29.0 29.0 0.0 100.0
-48 1 0.0 100.0 0.0 0.0 0.0 29.0 29.0 0.0 100.0
-49 1 100.0 0.0 0.0 0.0 0.0 29.0 29.0 0.0 100.0
-50 1 100.0 0.0 0.0 0.0 0.0 29.0 29.0 0.0 100.0
-51 1 0.0 100.0 0.0 0.0 0.0 29.0 29.0 0.0 100.0
-52 1 0.0 0.0 0.0 100.0 0.0 34.0 34.0 0.0 100.0
-53 1 0.0 100.0 0.0 0.0 0.0 34.0 34.0 0.0 100.0
-54 1 100.0 0.0 0.0 0.0 0.0 34.0 34.0 0.0 100.0
-55 1 0.0 100.0 0.0 0.0 0.0 34.0 34.0 0.0 100.0
-56 1 100.0 0.0 0.0 0.0 0.0 34.0 34.0 0.0 100.0
-57 1 0.0 0.0 100.0 0.0 0.0 34.0 34.0 0.0 100.0
-58 1 0.0 0.0 0.0 100.0 0.0 34.0 34.0 0.0 100.0
-59 1 0.0 0.0 0.0 100.0 0.0 21.0 21.0 0.0 100.0
-60 1 0.0 0.0 0.0 100.0 0.0 20.0 20.0 0.0 100.0
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_hety.fa
--- a/test-data/seqtk_hety.fa Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
->het_region
-ACTTTACATCGAGCMMMMMMMACAGTACTG
-
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_hety.out
--- a/test-data/seqtk_hety.out Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
-#chr start end A B num_het
-het_region 0 8 0.00 8 0
-het_region 8 9 0.00 8 0
-het_region 9 10 0.00 8 0
-het_region 10 11 0.00 8 0
-het_region 11 12 0.00 8 0
-het_region 12 13 0.00 8 0
-het_region 13 14 0.00 8 0
-het_region 14 15 1.00 8 1
-het_region 15 16 2.00 8 2
-het_region 16 17 3.00 8 3
-het_region 17 18 4.00 8 4
-het_region 18 19 5.00 8 5
-het_region 19 20 6.00 8 6
-het_region 20 21 7.00 8 7
-het_region 21 22 7.00 8 7
-het_region 22 23 6.00 8 6
-het_region 23 24 5.00 8 5
-het_region 24 25 4.00 8 4
-het_region 25 26 3.00 8 3
-het_region 26 27 2.00 8 2
-het_region 27 28 1.00 8 1
-het_region 28 29 0.00 8 0
-het_region 29 30 0.00 1 0
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_listhet.fa
--- a/test-data/seqtk_listhet.fa Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
->ambig
-ACGTMRWSYKVHDBN
-
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_listhet.out
--- a/test-data/seqtk_listhet.out Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-#chr position base
-ambig 5 M
-ambig 6 R
-ambig 7 W
-ambig 8 S
-ambig 9 Y
-ambig 10 K
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_mergefa.out
--- a/test-data/seqtk_mergefa.out Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
->test0
-ACTGAMTGMRN
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_mergefa1.fa
--- a/test-data/seqtk_mergefa1.fa Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
->test0
-ACTGACTGAAA
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_mergefa2.fa
--- a/test-data/seqtk_mergefa2.fa Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
->test0
-ACTGAMTGCGN
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_mergefa2.out
--- a/test-data/seqtk_mergefa2.out Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
->test0
-ACTGACTGxxa
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_mutfa.fa
--- a/test-data/seqtk_mutfa.fa Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
->test0
-ACTGACTGAA
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_mutfa.out
--- a/test-data/seqtk_mutfa.out Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
->test0
-GCTAACTGAA
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_mutfa.snp
--- a/test-data/seqtk_mutfa.snp Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-test0 1 . G
-test0 4 . A
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_randbase.fa
--- a/test-data/seqtk_randbase.fa Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
->ambig
-ACGTMRWSYK
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_randbase.out
--- a/test-data/seqtk_randbase.out Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
->ambig
-ACGTCGTGTT
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_sample.fa
--- a/test-data/seqtk_sample.fa Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,27 +0,0 @@
->seq0
-AAAAAAAAAA
-AAAAAAAAAA
->seq1
-TTTTTTTTTT
-TTTTTTTTTT
->seq2
-CCCCCCCCCC
-CCCCCCCCCC
->seq3
-GGGGGGGGGG
-GGGGGGGGGG
->seq4
-AAAAAAAAAA
-TTTTTTTTTT
->seq5
-AAAAAAAAAA
-CCCCCCCCCC
->seq6
-AAAAAAAAAA
-GGGGGGGGGG
->seq7
-TTTTTTTTTT
-CCCCCCCCCC
->seq8
-TTTTTTTTTT
-GGGGGGGGGG
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_sample.out
--- a/test-data/seqtk_sample.out Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
->seq7
-TTTTTTTTTTCCCCCCCCCC
->seq1
-TTTTTTTTTTTTTTTTTTTT
->seq4
-AAAAAAAAAATTTTTTTTTT
->seq3
-GGGGGGGGGGGGGGGGGGGG
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_seq.fa
--- a/test-data/seqtk_seq.fa Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
->test
-AACTGATCGATCGATCGNNNNNNNNNNNACATG
-
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_seq_revcom.fa
--- a/test-data/seqtk_seq_revcom.fa Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
->test
-CATGTNNNNNNNNNNNCGATCGATCGATCAGTT
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_subseq.fa
--- a/test-data/seqtk_subseq.fa Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
->seq1
-ACGTMRWSYK
->seq2
-RWSYKACGTM
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_subseq.out
--- a/test-data/seqtk_subseq.out Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
->seq1
-ACGTMRWSYK
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_subseq_list.txt
--- a/test-data/seqtk_subseq_list.txt Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-seq1
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_trimfq.fq
--- a/test-data/seqtk_trimfq.fq Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-@SEQ_ID1
-GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
-+
-!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_trimfq_be.fq
--- a/test-data/seqtk_trimfq_be.fq Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-@SEQ_ID1
-GGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCAC
-+
-(((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCC
diff -r 8a5151868549 -r fd11d2328ca8 test-data/seqtk_trimfq_default.fq
--- a/test-data/seqtk_trimfq_default.fq Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-@SEQ_ID1
-TAGTAAATCCATTTGTTCAACTCACAGTTT
-+
-*-+*''))**55CCF>>>>>>CCCCCCC65
diff -r 8a5151868549 -r fd11d2328ca8 tool_dependencies.xml
--- a/tool_dependencies.xml Wed Apr 29 12:07:03 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-
-
-
-
-
-