# HG changeset patch # User iuc # Date 1423155160 18000 # Node ID e0a0fd938de4762ede3d0c26aa0db7af4475a77b Uploaded diff -r 000000000000 -r e0a0fd938de4 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,33 @@ + + + + + seqtk + + + + 1.0-r75-dirty + + + + + + + + + + + + + + + + + `_, developed by Heng Li at the Broad Institute + ]]> + + diff -r 000000000000 -r e0a0fd938de4 seqtk_comp.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqtk_comp.xml Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,52 @@ + + + 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 000000000000 -r e0a0fd938de4 seqtk_cutN.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqtk_cutN.xml Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,52 @@ + + + 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 000000000000 -r e0a0fd938de4 seqtk_dropse.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqtk_dropse.xml Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,76 @@ + + + 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?>F + @test-6/2 + TGCGAAGACC + + + >2?A?A@@7? + @test-2/1 + AGACCAAAAT + + + ??><6E?IFC + @test-2/2 + CTGGCGAATT + + + ?=?*?A? + diff -r 000000000000 -r e0a0fd938de4 seqtk_fqchk.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqtk_fqchk.xml Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,58 @@ + + + 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 000000000000 -r e0a0fd938de4 seqtk_hety.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqtk_hety.xml Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,73 @@ + + + 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 000000000000 -r e0a0fd938de4 seqtk_listhet.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqtk_listhet.xml Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,47 @@ + + + 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 000000000000 -r e0a0fd938de4 seqtk_mergefa.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqtk_mergefa.xml Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,68 @@ + + + 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 000000000000 -r e0a0fd938de4 seqtk_mergepe.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqtk_mergepe.xml Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,93 @@ + + + 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 000000000000 -r e0a0fd938de4 seqtk_mutfa.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqtk_mutfa.xml Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,51 @@ + + + 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 000000000000 -r e0a0fd938de4 seqtk_randbase.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqtk_randbase.xml Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,45 @@ + + + choose a random base from hets + + macros.xml + + + + $default]]> + + + + + + + + + + + + ambig + ACGTMRWSYK + +results in + +:: + + # Output result + >ambig + ACGTCGTGTT + +@ATTRIBUTION@ +]]> + diff -r 000000000000 -r e0a0fd938de4 seqtk_sample.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqtk_sample.xml Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,38 @@ + + + + + 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 000000000000 -r e0a0fd938de4 seqtk_seq.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqtk_seq.xml Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,76 @@ + + + common transformation of FASTA/Q + + macros.xml + + + + $default]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r e0a0fd938de4 seqtk_subseq.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqtk_subseq.xml Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,83 @@ + + + extract subsequences from FASTA/Q files + + macros.xml + + + + $default]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + seq1 + ACGTMRWSYK + >seq2 + RWSYKACGTM + +results in + +:: + + # Output result + >seq1 + ACGTMRWSYK + +@ATTRIBUTION@ +]]> + diff -r 000000000000 -r e0a0fd938de4 seqtk_trimfq.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqtk_trimfq.xml Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,62 @@ + + + trim FASTQ using the Phred algorithm + + macros.xml + + + + $default]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r e0a0fd938de4 test-data/paired_dat.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired_dat.fq Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,24 @@ +@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?>F +@test-4/1 +CTTGACGCTG ++ +I@>3EFCG@C +@test-2/1 +AGACCAAAAT ++ +??><6E?IFC diff -r 000000000000 -r e0a0fd938de4 test-data/paired_dat2.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired_dat2.fq Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,12 @@ +@test-6/2 +TGCGAAGACC ++ +>2?A?A@@7? +@test-4/2 +TGCGAAGACC ++ +A?A@@B@test0 +ACTGACTGAA +>ambig_ref +ACGTCGTGTTVHDBN + diff -r 000000000000 -r e0a0fd938de4 test-data/seqtk_comp.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_comp.out Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,3 @@ +#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 000000000000 -r e0a0fd938de4 test-data/seqtk_cutn.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_cutn.fa Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,3 @@ +>test +AACTGATCGATCGATCGNNNNNNNNNNNACATG + diff -r 000000000000 -r e0a0fd938de4 test-data/seqtk_cutn.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_cutn.out Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,4 @@ +>test:1-17 +AACTGATCGATCGATCG +>test:29-33 +ACATG diff -r 000000000000 -r e0a0fd938de4 test-data/seqtk_dropse.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_dropse.fq Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,20 @@ +@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?>F +@test-6/2 +TGCGAAGACC ++ +>2?A?A@@7? +@test-2/1 +AGACCAAAAT ++ +??><6E?IFC +@test-2/2 +CTGGCGAATT ++ +?=?*?A?>>>>>CCCCCCC65 diff -r 000000000000 -r e0a0fd938de4 test-data/seqtk_fqchk.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_fqchk.out Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,63 @@ +#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 000000000000 -r e0a0fd938de4 test-data/seqtk_hety.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_hety.fa Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,3 @@ +>het_region +ACTTTACATCGAGCMMMMMMMACAGTACTG + diff -r 000000000000 -r e0a0fd938de4 test-data/seqtk_hety.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_hety.out Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,24 @@ +#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 000000000000 -r e0a0fd938de4 test-data/seqtk_listhet.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_listhet.fa Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,3 @@ +>ambig +ACGTMRWSYKVHDBN + diff -r 000000000000 -r e0a0fd938de4 test-data/seqtk_listhet.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_listhet.out Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,7 @@ +#chr position base +ambig 5 M +ambig 6 R +ambig 7 W +ambig 8 S +ambig 9 Y +ambig 10 K diff -r 000000000000 -r e0a0fd938de4 test-data/seqtk_mergefa.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_mergefa.out Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,2 @@ +>test0 +ACTGAMTGMRN diff -r 000000000000 -r e0a0fd938de4 test-data/seqtk_mergefa1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_mergefa1.fa Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,2 @@ +>test0 +ACTGACTGAAA diff -r 000000000000 -r e0a0fd938de4 test-data/seqtk_mergefa2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_mergefa2.fa Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,2 @@ +>test0 +ACTGAMTGCGN diff -r 000000000000 -r e0a0fd938de4 test-data/seqtk_mergefa2.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_mergefa2.out Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,2 @@ +>test0 +ACTGACTGxxa diff -r 000000000000 -r e0a0fd938de4 test-data/seqtk_mutfa.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_mutfa.fa Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,2 @@ +>test0 +ACTGACTGAA diff -r 000000000000 -r e0a0fd938de4 test-data/seqtk_mutfa.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_mutfa.out Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,2 @@ +>test0 +GCTAACTGAA diff -r 000000000000 -r e0a0fd938de4 test-data/seqtk_mutfa.snp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_mutfa.snp Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,2 @@ +test0 1 . G +test0 4 . A diff -r 000000000000 -r e0a0fd938de4 test-data/seqtk_randbase.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_randbase.fa Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,2 @@ +>ambig +ACGTMRWSYK diff -r 000000000000 -r e0a0fd938de4 test-data/seqtk_randbase.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_randbase.out Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,2 @@ +>ambig +ACGTCGTGTT diff -r 000000000000 -r e0a0fd938de4 test-data/seqtk_sample.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_sample.fa Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,27 @@ +>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 000000000000 -r e0a0fd938de4 test-data/seqtk_sample.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_sample.out Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,8 @@ +>seq7 +TTTTTTTTTTCCCCCCCCCC +>seq1 +TTTTTTTTTTTTTTTTTTTT +>seq4 +AAAAAAAAAATTTTTTTTTT +>seq3 +GGGGGGGGGGGGGGGGGGGG diff -r 000000000000 -r e0a0fd938de4 test-data/seqtk_seq.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_seq.fa Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,3 @@ +>test +AACTGATCGATCGATCGNNNNNNNNNNNACATG + diff -r 000000000000 -r e0a0fd938de4 test-data/seqtk_seq_revcom.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_seq_revcom.fa Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,2 @@ +>test +CATGTNNNNNNNNNNNCGATCGATCGATCAGTT diff -r 000000000000 -r e0a0fd938de4 test-data/seqtk_subseq.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_subseq.fa Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,4 @@ +>seq1 +ACGTMRWSYK +>seq2 +RWSYKACGTM diff -r 000000000000 -r e0a0fd938de4 test-data/seqtk_subseq.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_subseq.out Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,2 @@ +>seq1 +ACGTMRWSYK diff -r 000000000000 -r e0a0fd938de4 test-data/seqtk_subseq_list.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_subseq_list.txt Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,1 @@ +seq1 diff -r 000000000000 -r e0a0fd938de4 test-data/seqtk_trimfq.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_trimfq.fq Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,4 @@ +@SEQ_ID1 +GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT ++ +!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65 diff -r 000000000000 -r e0a0fd938de4 test-data/seqtk_trimfq_be.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_trimfq_be.fq Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,4 @@ +@SEQ_ID1 +GGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCAC ++ +(((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCC diff -r 000000000000 -r e0a0fd938de4 test-data/seqtk_trimfq_default.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_trimfq_default.fq Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,4 @@ +@SEQ_ID1 +TAGTAAATCCATTTGTTCAACTCACAGTTT ++ +*-+*''))**55CCF>>>>>>CCCCCCC65 diff -r 000000000000 -r e0a0fd938de4 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,6 @@ + + + + + +