| Next changeset 1:8076141a76a7 (2018-04-18) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48 |
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added:
extract_aln_ends.xml macros.xml test-data/converted_bcs.fastq test-data/extracted_bcs.fastq test-data/merged_pcr_dupes.bed test-data/merged_pcr_dupes_clnts.bed test-data/merged_pcr_dupes_spurious.bed test-data/merged_pcr_dupes_spurious_filtered_thresh05.bed test-data/pcr_dupes_randomdict.fastq test-data/pcr_dupes_sorted_2.bed test-data/reads.fastq test-data/readswithtail.fastq test-data/readswithtailremoved.fastq test-data/result_original_head.fastq test-data/twomates.sam test-data/tworeads_aln_ends.bed |
| b |
| diff -r 000000000000 -r 0e70f9058b02 extract_aln_ends.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extract_aln_ends.xml Tue Nov 14 05:53:02 2017 -0500 |
| [ |
| @@ -0,0 +1,49 @@ +<tool id="bctools_extract_alignment_ends" name="Extract alignment ends" version="@VERSION@"> + <description>from SAM or BAM</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + extract_aln_ends.py + '$alignments' + > '$alignment_ends' + ]]></command> + <inputs> + <param name="alignments" type="data" format="sam,bam" label="Alignments in SAM or BAM format"/> + </inputs> + <outputs> + <data name="alignment_ends" format="bed"/> + </outputs> + <tests> + <test> + <param name="alignments" value="twomates.sam"/> + <output name="alignment_ends" file="tworeads_aln_ends.bed"/> + </test> + </tests> + <help><![CDATA[ + +bctools - Extract alignment ends from from SAM or BAM alignments +================================================================ + +The resulting BED file contains the outer coordinates of the alignments. The BED +name field is set to the read id and the score field is set to the edit distance +of the alignment. The crosslinked nucleotide is one nt upstream of the 5'-end of +the BED entries. + +This tool only reports results for alignments that are properly aligned in FR +("forward-reverse") direction. + +Input: +------ + +* BAM file containing alignments (paired-end sequencing) + +Output: +------- + +* BED file containing outer coordinates (sorted by read id) + + ]]></help> + <expand macro="citations"/> +</tool> |
| b |
| diff -r 000000000000 -r 0e70f9058b02 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Nov 14 05:53:02 2017 -0500 |
| b |
| @@ -0,0 +1,13 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">bctools</requirement> + </requirements> + </xml> + <token name="@VERSION@">0.2.1</token> + <xml name="citations"> + <citations> + <citation type="doi">10.1016/j.molcel.2013.07.001</citation> + </citations> + </xml> +</macros> |
| b |
| diff -r 000000000000 -r 0e70f9058b02 test-data/converted_bcs.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/converted_bcs.fastq Tue Nov 14 05:53:02 2017 -0500 |
| b |
| @@ -0,0 +1,400 @@ +@UID0 +NYYRRY ++ +#0<FFF +@UID1 +RRYRYR ++ +BBBFFF +@UID2 +RYYRRY ++ +B<BF<B +@UID3 +YRYRYR ++ +BBBFFF +@UID4 +NRRRRY ++ +#0<FFF +@UID5 +RRRRRY ++ +BBBFFF +@UID6 +YRRRYR ++ +BBBFFF +@UID7 +NYYRRY ++ +#0<FFF +@UID8 +RYRRRY ++ +BBBFFF +@UID9 +RRRRRY ++ +BBBFFF +@UID10 +NRRRRY ++ +#0<FFF +@UID11 +NYRRYR ++ +#0<FFF +@UID12 +NRYRRY ++ +#0<FFF +@UID13 +NRRRRY ++ +#0<FFF +@UID14 +YYRRYR ++ +BBBFFF +@UID15 +YYRRRY ++ +BBBFFF +@UID16 +YYYRYR ++ +BBBFFF +@UID17 +YRRRYR ++ +BBBFFF +@UID18 +RYYRRY ++ +BBBFFF +@UID19 +RYYYYY ++ +BBBFFF +@UID20 +RYRRYR ++ +BBBFFF +@UID21 +RYRRYR ++ +BBBFFF +@UID22 +YYRRYR ++ +BBBFFF +@UID23 +YYYRYR ++ +BBBFFF +@UID24 +YRRRYR ++ +BBBFFF +@UID25 +RRYYRR ++ +BBBFFF +@UID26 +YYRRRY ++ +BBBFFB +@UID27 +RYYRRY ++ +BBBFFF +@UID28 +RYYRYR ++ +BBBFFF +@UID29 +NYYRYR ++ +#0<FFF +@UID30 +NYRRYR ++ +#0<FFF +@UID31 +YRYRRY ++ +BBBFFF +@UID32 +YRYRRY ++ +BBBFFF +@UID33 +RYYRRY ++ +BBBFFF +@UID34 +RRRRYR ++ +BBBFFF +@UID35 +NYYRRY ++ +#0<FFF +@UID36 +YYRRYR ++ +BBBFFF +@UID37 +RRRRRY ++ +BBBFFF +@UID38 +RRRRRY ++ +BBBFFF +@UID39 +YYRRRY ++ +BBBFFF +@UID40 +YYRRRY ++ +BBBFFF +@UID41 +RYYRYR ++ +BBBFFF +@UID42 +YRYRYR ++ +BBBFFF +@UID43 +RRRRYR ++ +BBBFFF +@UID44 +RYRRYR ++ +BBBFFF +@UID45 +NYYRRY ++ +#0<FBF +@UID46 +YYYRYR ++ +BBBFFF +@UID47 +RRRRRY ++ +BBBFFF +@UID48 +RYRRRY ++ +BBBFFF +@UID49 +RYRRYR ++ +BBBFFF +@UID50 +RYYRRY ++ +BBBFFF +@UID51 +YRYYRR ++ +BBBFFF +@UID52 +RYRRRY ++ +BBBFFF +@UID53 +RRRRRY ++ +BBBF<F +@UID54 +YYRRRY ++ +BBBFFF +@UID55 +RYYRRY ++ +BBBFFF +@UID56 +YYYRRY ++ +BBBFFF +@UID57 +NYYYRY ++ +#0BFFF +@UID58 +NRRRRY ++ +#0<FFF +@UID59 +NYRRRY ++ +#0<FFF +@UID60 +RRYRRY ++ +BB<FFF +@UID61 +RRRRYR ++ +BBBFFF +@UID62 +YRRRRY ++ +BBBFFF +@UID63 +RRRRRY ++ +BBBFFF +@UID64 +YRRRYR ++ +BBBFFF +@UID65 +RRYRYR ++ +BBBFFF +@UID66 +RRRRRY ++ +BBBFFF +@UID67 +RRYRYR ++ +BB<FFF +@UID68 +NYYRRY ++ +#00FFF +@UID69 +YYRRRY ++ +BBBFFF +@UID70 +YYYRYR ++ +BBBFFF +@UID71 +RRRRYR ++ +BBBFFF +@UID72 +RRRRYR ++ +BBBFFF +@UID73 +NRYRYR ++ +#0<BFF +@UID74 +YYYRYY ++ +BBBFFF +@UID75 +YYRRRY ++ +BBBFFF +@UID76 +YRRRRY ++ +BBBFFF +@UID77 +NRYRYR ++ +#0<FFF +@UID78 +NRRRRY ++ +#0<FFF +@UID79 +YYYRRY ++ +BBBFFF +@UID80 +RYYRRY ++ +BBBFFF +@UID81 +NYYRYR ++ +#0<FFF +@UID82 +NRRRRY ++ +#0<FFF +@UID83 +NYRRRY ++ +#0<FFF +@UID84 +NRRRRY ++ +#0<FFF +@UID85 +RYRRRY ++ +BBBFFF +@UID86 +RRRRRY ++ +BBBFFF +@UID87 +NRYRRY ++ +#0<FFF +@UID88 +NRRRRY ++ +#0<FFF +@UID89 +NYRRRY ++ +#0<FFF +@UID90 +NRYRRY ++ +#0<FFF +@UID91 +RRRRYR ++ +BBBFFF +@UID92 +RRRRYR ++ +BBBFFF +@UID93 +YRYRRY ++ +BBBFFF +@UID94 +RRYRYR ++ +BBBFFF +@UID95 +RYRRYR ++ +BBBFFF +@UID96 +NYRRRY ++ +#0<FFF +@UID97 +NYYRRY ++ +#0<FFF +@UID98 +YYRRRY ++ +BBBFFF +@UID99 +YRYRYR ++ +BBBFFF |
| b |
| diff -r 000000000000 -r 0e70f9058b02 test-data/extracted_bcs.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/extracted_bcs.fastq Tue Nov 14 05:53:02 2017 -0500 |
| b |
| @@ -0,0 +1,400 @@ +@UID0 +NCTAAT ++ +#0<FFF +@UID1 +GGTACG ++ +BBBFFF +@UID2 +GCTAAT ++ +B<BF<B +@UID3 +CATACG ++ +BBBFFF +@UID4 +NAAAAT ++ +#0<FFF +@UID5 +AAGAAT ++ +BBBFFF +@UID6 +CAAACG ++ +BBBFFF +@UID7 +NCCGGT ++ +#0<FFF +@UID8 +ACAAAT ++ +BBBFFF +@UID9 +AAGAAT ++ +BBBFFF +@UID10 +NAAAAT ++ +#0<FFF +@UID11 +NCAACG ++ +#0<FFF +@UID12 +NGCAAT ++ +#0<FFF +@UID13 +NAGAAT ++ +#0<FFF +@UID14 +TCAACG ++ +BBBFFF +@UID15 +TCGAAT ++ +BBBFFF +@UID16 +CCCGCG ++ +BBBFFF +@UID17 +CAAGCG ++ +BBBFFF +@UID18 +ACCAAT ++ +BBBFFF +@UID19 +ACTCTT ++ +BBBFFF +@UID20 +GCAACG ++ +BBBFFF +@UID21 +ACGACG ++ +BBBFFF +@UID22 +TCAGCG ++ +BBBFFF +@UID23 +TTCACG ++ +BBBFFF +@UID24 +TAAACG ++ +BBBFFF +@UID25 +GATTGA ++ +BBBFFF +@UID26 +TCAGGT ++ +BBBFFB +@UID27 +ACTAAT ++ +BBBFFF +@UID28 +ACTACG ++ +BBBFFF +@UID29 +NTTGCG ++ +#0<FFF +@UID30 +NCAACG ++ +#0<FFF +@UID31 +CACAAT ++ +BBBFFF +@UID32 +CACAAT ++ +BBBFFF +@UID33 +GCCAAT ++ +BBBFFF +@UID34 +AGAACG ++ +BBBFFF +@UID35 +NTTAAT ++ +#0<FFF +@UID36 +CTAGCG ++ +BBBFFF +@UID37 +GAGAAT ++ +BBBFFF +@UID38 +AGGAAT ++ +BBBFFF +@UID39 +CCAAAT ++ +BBBFFF +@UID40 +CCAAAT ++ +BBBFFF +@UID41 +ACTGCG ++ +BBBFFF +@UID42 +TACGCG ++ +BBBFFF +@UID43 +GGGACG ++ +BBBFFF +@UID44 +GCAACG ++ +BBBFFF +@UID45 +NCTAAT ++ +#0<FBF +@UID46 +CCCGCG ++ +BBBFFF +@UID47 +AAGAAT ++ +BBBFFF +@UID48 +ATAAAT ++ +BBBFFF +@UID49 +ACAGCG ++ +BBBFFF +@UID50 +ACTGGT ++ +BBBFFF +@UID51 +CACTGA ++ +BBBFFF +@UID52 +GCGAAT ++ +BBBFFF +@UID53 +GAAAAT ++ +BBBF<F +@UID54 +CCAAAT ++ +BBBFFF +@UID55 +ACCAAT ++ +BBBFFF +@UID56 +TCCAAT ++ +BBBFFF +@UID57 +NCCCAC ++ +#0BFFF +@UID58 +NAGAAT ++ +#0<FFF +@UID59 +NTAAAT ++ +#0<FFF +@UID60 +GACAAT ++ +BB<FFF +@UID61 +GGGGCG ++ +BBBFFF +@UID62 +CAAAAT ++ +BBBFFF +@UID63 +AAAAAT ++ +BBBFFF +@UID64 +TAGACG ++ +BBBFFF +@UID65 +AGCACG ++ +BBBFFF +@UID66 +AGGAAT ++ +BBBFFF +@UID67 +AACACG ++ +BB<FFF +@UID68 +NCCAAT ++ +#00FFF +@UID69 +CTGGGT ++ +BBBFFF +@UID70 +TCTACG ++ +BBBFFF +@UID71 +AAAACG ++ +BBBFFF +@UID72 +GGAATA ++ +BBBFFF +@UID73 +NACGCG ++ +#0<BFF +@UID74 +TCTACC ++ +BBBFFF +@UID75 +CCAAAT ++ +BBBFFF +@UID76 +TGAAAT ++ +BBBFFF +@UID77 +NGTACG ++ +#0<FFF +@UID78 +NAAAAT ++ +#0<FFF +@UID79 +TTTAAT ++ +BBBFFF +@UID80 +ACCAAT ++ +BBBFFF +@UID81 +NCCACG ++ +#0<FFF +@UID82 +NAGAAT ++ +#0<FFF +@UID83 +NTAAAT ++ +#0<FFF +@UID84 +NAAAAT ++ +#0<FFF +@UID85 +ACAAAT ++ +BBBFFF +@UID86 +AAGAAT ++ +BBBFFF +@UID87 +NATAAT ++ +#0<FFF +@UID88 +NAAAAT ++ +#0<FFF +@UID89 +NCGAAT ++ +#0<FFF +@UID90 +NGCAAT ++ +#0<FFF +@UID91 +AAGGCG ++ +BBBFFF +@UID92 +AAGACG ++ +BBBFFF +@UID93 +CATAAT ++ +BBBFFF +@UID94 +AATACG ++ +BBBFFF +@UID95 +GCAACG ++ +BBBFFF +@UID96 +NCAAAT ++ +#0<FFF +@UID97 +NCCAAT ++ +#0<FFF +@UID98 +CCAAAT ++ +BBBFFF +@UID99 +TATGCG ++ +BBBFFF |
| b |
| diff -r 000000000000 -r 0e70f9058b02 test-data/merged_pcr_dupes.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/merged_pcr_dupes.bed Tue Nov 14 05:53:02 2017 -0500 |
| b |
| @@ -0,0 +1,3 @@ +chr1 10 20 readid_11 10 + +chr1 10 20 readid_0 5 - +chrX 20 30 readid_10 7 + |
| b |
| diff -r 000000000000 -r 0e70f9058b02 test-data/merged_pcr_dupes_clnts.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/merged_pcr_dupes_clnts.bed Tue Nov 14 05:53:02 2017 -0500 |
| b |
| @@ -0,0 +1,3 @@ +chr1 9 10 readid_11 10 + +chr1 20 21 readid_0 5 - +chrX 19 20 readid_10 7 + |
| b |
| diff -r 000000000000 -r 0e70f9058b02 test-data/merged_pcr_dupes_spurious.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/merged_pcr_dupes_spurious.bed Tue Nov 14 05:53:02 2017 -0500 |
| b |
| @@ -0,0 +1,12 @@ +chr1 10 20 AAAAA 1 + +chr1 10 20 AAAAA 2 + +chr1 10 20 AAAAA 3 + +chr1 10 20 AAAAA 4 + +chr1 10 20 AAAAA 5 + +chr1 10 20 AAAAA 10 + +chr1 10 20 AAAAA 100 + +chr1 10 20 AAAAA 3 - +chr1 10 20 AAAAA 5 - +chr1 10 20 AAAAA 4 - +chr1 10 20 AAAAA 5 - +chrX 20 30 TTTTT 7 + |
| b |
| diff -r 000000000000 -r 0e70f9058b02 test-data/merged_pcr_dupes_spurious_filtered_thresh05.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/merged_pcr_dupes_spurious_filtered_thresh05.bed Tue Nov 14 05:53:02 2017 -0500 |
| b |
| @@ -0,0 +1,6 @@ +chr1 10 20 AAAAA 5 - +chr1 10 20 AAAAA 5 - +chr1 10 20 AAAAA 4 - +chr1 10 20 AAAAA 3 - +chr1 10 20 AAAAA 100 + +chrX 20 30 TTTTT 7 + |
| b |
| diff -r 000000000000 -r 0e70f9058b02 test-data/pcr_dupes_randomdict.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pcr_dupes_randomdict.fastq Tue Nov 14 05:53:02 2017 -0500 |
| b |
| @@ -0,0 +1,88 @@ +@readid_0 +AAAAA ++ +BBBBB +@readid_1 +AAAAA ++ +BBBBB +@readid_2 +AAAAA ++ +BBBBB +@readid_3 +TTTTT ++ +BBBBB +@readid_4 +AAAAA ++ +BBBBB +@readid_5 +AAAAA ++ +BBBBB +@readid_6 +AAAAA ++ +BBBBB +@readid_7 +TTTTT ++ +BBBBB +@readid_8 +AAAAA ++ +BBBBB +@readid_9 +AAAAA ++ +BBBBB +@readid_10 +TTTTT ++ +BBBBB +@readid_11 +AAAAA ++ +BBBBB +@readid_12 +TTTTT ++ +BBBBB +@readid_13 +TTTTT ++ +BBBBB +@readid_14 +TTTTT ++ +BBBBB +@readid_15 +AAAAA ++ +BBBBB +@readid_16 +AAAAA ++ +BBBBB +@readid_17 +AAAAA ++ +BBBBB +@readid_18 +AAAAA ++ +BBBBB +@readid_19 +AAAAA ++ +BBBBB +@readid_20 +TTTTT ++ +BBBBB +@readid_21 +AAAAA ++ +BBBBB |
| b |
| diff -r 000000000000 -r 0e70f9058b02 test-data/pcr_dupes_sorted_2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pcr_dupes_sorted_2.bed Tue Nov 14 05:53:02 2017 -0500 |
| b |
| @@ -0,0 +1,22 @@ +chr1 10 20 readid_0 0 - +chr1 10 20 readid_1 0 - +chr1 10 20 readid_2 0 + +chr1 10 20 readid_4 0 + +chr1 10 20 readid_5 0 + +chr1 10 20 readid_6 0 - +chr1 10 20 readid_8 0 + +chr1 10 20 readid_9 0 - +chr1 10 20 readid_11 0 + +chr1 10 20 readid_15 0 + +chr1 10 20 readid_16 0 + +chr1 10 20 readid_17 0 - +chr1 10 20 readid_18 0 + +chr1 10 20 readid_19 0 + +chr1 10 20 readid_21 0 + +chrX 20 30 readid_3 0 + +chrX 20 30 readid_7 0 + +chrX 20 30 readid_10 0 + +chrX 20 30 readid_12 0 + +chrX 20 30 readid_13 0 + +chrX 20 30 readid_14 0 + +chrX 20 30 readid_20 0 + |
| b |
| diff -r 000000000000 -r 0e70f9058b02 test-data/reads.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads.fastq Tue Nov 14 05:53:02 2017 -0500 |
| b |
| b"@@ -0,0 +1,400 @@\n+@UID0\n+NCTAGAATGAAAAATGTATGCTTGTGACCAATAAATATAAAAGGTTAAGATCGGAAGAGCACACGTCTG\n++\n+#0<FFFFFFFFFFFFIFIIIIIIIIIIIIIIFIIIIIIFIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@UID1\n+GGTTAACGCCAGTTGGTCCGAGTGTTGTGGGTTATTGTTAACTAAGATCGGAAGAGCACACGTCTGAAC\n++\n+BBBFFFFFFFFFFIIIIIIIFFFFFIIIIIIFIFIIIIIIIIIFFIFIIIIFFIIFFFFFFFFFFFBFB\n+@UID2\n+GCTAGAATCCTTTTCCTTTGCCCTGATCTTGTCGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT\n++\n+B<B<BF<BFBFBFIFFFBFFFFFFFBBB0BBFFFBB<FB707'BFF0FFB'<B<BF#############\n+@UID3\n+CATTCACGTGGTTGGCGTTTGGTGTGTGGCTGTTTCTGCTCATTGATAGATCGGAAGAGCACACGTCTG\n++\n+BBBFFFFFFFFFFIIFFFFIIIFFFFFFIFIIFIIFFIFIIIFIIFFIIIIFIIFFFFFFFFFFFFBFF\n+@UID4\n+NAAAGAATACTGCTTTAATTCTAAATAAAAATTTATTGCCAAGATCGGAAGAGCACACGTCTGAACTCC\n++\n+#0<BFFFFFFFFFIIIFFFIIIIIIFIIFIFFIFIIIIFFIIIIIIIIIIIBFFFIIIIIIIIFIIIFF\n+@UID5\n+AAGAGAATGAATTGCCCCCCCCCACAACCGCGCTTGACTAGCGTAGCAGATCGGAAGAGCACACGTCTG\n++\n+BBBFFFFFFFFFFI0<FFFFIIIIIIIIIIIFBFFBFFFFBBFBFFFBBFFFFFFFFBBBFBFFFBBBB\n+@UID6\n+CAATCACGAAGTGTCCTCAGCAAAAGCTGGGTGGTTACCAAGATCGGAAGAGCACACGTCTGAACTCCA\n++\n+BBBFFFFFFFFFFFFFFIIIIIIFIFFIIIIBFFIIBBF<BFBFFFFIII7FFBFFFFBBBBBBFF<<B\n+@UID7\n+NCCGAGGTCAATCCGAGTCACGGCACCATGTTAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTC\n++\n+#0<FFFFFFFFFFIIIIFIIIIIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFFB\n+@UID8\n+ACAAGAATAATCTTCTTAGAGTTGGTTAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCATTCA\n++\n+BBBFFFFFFFFFFIFFIFI<FBFFFFFFIFFFFFFIBFBBFBFFFFFFFFFBBFFBB<7BFFF<<BB<B\n+@UID9\n+AAGAGAATAAATTACTAAATGTGAAAAACATAATGTGAAAAGTATATGTTAAGATCGGAAGAGCACACG\n++\n+BBBFFFFFFFFFFIIIIFFIIFIFIFIIFIFFFFF<BFFFIFFFIIIIIIIFFFIFF<FIIIIIIFIFI\n+@UID10\n+NAAAGAATGACCTGTAAACAGAATGATAAAGTATGTGATAGATCGGAAGAGCACACGTCTGAACTCCAG\n++\n+#0<FFFFFFFFFFIIIIIIIIIIIIIIIIIIFFIIFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@UID11\n+NCATCACGAATCTGGCATGTTGGAACAATGTAGGTAAGGGAAGTGGTCAAGATCGGAAGAGCACACGTC\n++\n+#0<FFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIFFIIIIFIIFIIFIIIIIIIIIIIIIIIIIIFFFF\n+@UID12\n+NGCAGAATGGTTAAAGTTGCTGGCCTAATGAGCTCAGTAGATCGGAAGAGCACACGTCTGAACTCCAGT\n++\n+#0<FFFFFFFFFFIIIIIIIIIIIIIFFIIIIIIIIIIIIIIIIIIIIIFFIIIIIIIIIFIIIIIIIF\n+@UID13\n+NAGAGAATAAATCTTATTAATTCCCTCAAAAGCAGGTTAAGATCGGAAGAGCACACGTCTGAACTCCAG\n++\n+#0<FFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIF\n+@UID14\n+TCATCACGATGGTTGAGATCGGAAAGCACTATCGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIFIIIIFIFIIIIIIIIIIIIIIIFFIFFFFFFFFFBFBFF\n+@UID15\n+TCGAGAATCCGCCCACCCAGGGACGCCAGGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCA\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFFFFFBFFFFFF\n+@UID16\n+CCCCGGCGCTATCCCACTTCTGACACCAGGCTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTC\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFFFFFFFFFB\n+@UID17\n+CAACGGCGGAGTCTGTTATAAAATGGACTTAACTGCCGAGATCGGAAGAGCACACGTCTGAACTCCAGT\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIFIIIIIIIIIIIIFFFFFFFFFFFFFFFFFFFFFFFFFFFBFF\n+@UID18\n+ACCAGAATCCGTCTAGAATGTAGCATCTAGTGACTTTTTAAAGCCGGTTAAGATCGGAAGAGCACACGT\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFF\n+@UID19\n+ACTTTCTTTCCTGGGCATCCCGGGGATCCCAGAGCCGGCCCAGGTAGGCCAAGATCGGAAGAGCACACG\n++\n+BBBFFFFFFFFFFIIFIIIIIIFFFIIIIIIIIIIIFIIBFIIIBBFFFFBFFFFFFFFFBFFBFBFFF\n+@UID20\n+GCATCACGGGCCTACTCTACTTTCTGTTGCCGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCA\n++\n+BBBFFFFFFFFFFFIFIIIIIIIIIFFFFIIIIIIFFFIFF<FFFFFFF<<BFBFFFFFFFBBBBFFFB\n+@UID21\n+ACGTCACGCAATCATGTTCGCCTCACACGCGAAAGGTCTTGACAGATCGGAAGAGCACACGTCTGAACT\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIFFIIIIIIIIFFFFFFFFFFFFFFFFFFFFFFF\n+@UID22\n+TCACGGCGCGACCTAATGTTAGTGAATATTACTAAGTTGCCAAGATCGGAAGAGCACACGTCTGAACTC\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFFFFFF\n+@UID23\n+TTCTCACGGCGGTGGGATCCCGCGGCCACAGTAGATCGGGAGAGCACACGTCTGAACTCCAGTCACTCA\n++\n+BBBFFFFFFFFFBBFF0'BFF<B<B7B0<7<'<<7'7<<'0'7<7<<<7'0<<<<B'0<B'00<BB###\n+@UID24\n+TAATCACGCGACAGCCACAAGTTACATAGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCATT\n++\n+BBBFFFFFFFFFFIIIIIIIIFIIIIIIIIIIIIIIIIIIIIFIIIIIIIFFFFFFFFFFFFFFFFFFF\n+@UID25\n+GATGCTGAACTCTCGTAGTTGGATCTTGGGAGCGGGCGGGCGGCTAAGATCGGAAGAGCACACGTCTGA\n++\n+BBBFFFFFFFBFFFFIIFFIFFFFFFFFFFFFFFFFBBF7BB7BFFBFBBBBBFB7BBFFFFBFB<BBB\n+@UID26\n+TCAG"..b'BBFFBBBFBFFFBFFBBFBB\n+@UID74\n+TCTTCACCGCATCCAGATTCTGTAGAGCTGGACAGGCAGGTGGTAGATCGGAAGAGCACACGTCTGAAC\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIBFFFFFIIIIIIIFIIIIIIFFFFFFFFF\n+@UID75\n+CCAAGAATCCTTAACATTTTATTATTTATTGTAAAATCAATTTGTGACAGATCGGAAGAGCACACGTCT\n++\n+BBBFFFFFFFFFFIIFFFIIIIIIFIIFFIIFFIIFBFF<FIBFBBBFB7BFFFB<FFIFIIFFFFIBF\n+@UID76\n+TGAAGAATGATTTTAACCTGCAATTTGCCTCAGCAACAGGTTAAGATCGGAAGAGCACACGTCTGAACT\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIIIIIIIIIIIIF\n+@UID77\n+NGTTCACGGGCTCCTCCCCTTCGTCTTCACAGAGCTGGTCAAGATCGGAAGAGCACACGTCTGAACTCC\n++\n+#0<FFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIIFFFFFFFFFFFFF\n+@UID78\n+NAAAGAATGATTTATAACCACAACAAGAAGGGAATCAATGTTAAGATCGGAAGAGCACACGTCTGAACT\n++\n+#0<FFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFF\n+@UID79\n+TTTAGAATCAATGACCAATTACCAAGGAAGCTAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTC\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFF\n+@UID80\n+ACCAGAATCCTCACCCTAACACCCTTCAATACAATGTTTACAGGGTTAAGATCGGAAGAGCACACGTCT\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFIIIIIIIIIIIIIIIIIIFFFF\n+@UID81\n+NCCTCACGACTTTGTTAAGTTGATTTAACATTGCCCCCCCCACAACTTGGCAGATCGGAAGAGCACACG\n++\n+#0<FFFFFFFFFFIIIIIIFIIIIIIIIIIIFFFIIIIIIIIIFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@UID82\n+NAGAGAATGATTTTAACTAAGGTGGTGACACTGGTAACAGATCGGAAGAGCACACGTCTGAACTCCAGT\n++\n+#0<FFFFFFFFFFIIIIIIIIIFFFFFFIIIIIIFFIIIIIIIIIIIFFFIIIIIFFFIIIIIIIIFFF\n+@UID83\n+NTAAGAATAAAATAAGTGTGATCAATCTTTTTGTCGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA\n++\n+#0<FFFFFFFFFFIIIFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFF\n+@UID84\n+NAAAGAATAATTTGACAACTTTAAATGAGTGTAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC\n++\n+#0<FFFFFFFFFFIIIIIIIFIIFIIIIIIIFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIF\n+@UID85\n+ACAAGAATAAGTTATTCCTTTAAAAGAAATTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT\n++\n+BBBBBFFFFFFFBFFIFFFIFFFFFFBFFFFFIIFFFIFFIBFBBB<FFBBB<BFFFFB<BBFBBFFFB\n+@UID86\n+AAGAGAATAAGCTAGAGCAGGCCTGCTTGCGGCTCCCTGTGGTTAAGATCGGAAGAGCACACGTTGAAC\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIIIIIIIIIFFFFFFFFFFFFFF\n+@UID87\n+NATAGAATAACTTAAATTGATTAAAACTTTGTAGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC\n++\n+#0<FFFFFFFFFFIIIIIIIIIIIIIIIIIIFIIFIIIIIIIIIFIIIIIIIIIIIIFIIIIIIIIIIF\n+@UID88\n+NAAAGAATCGATCTCGGTGGAACCTCCAGGTTAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTC\n++\n+#0<FFFFFFFFFFIIIIIIIIIIIIIIIIIFFIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFB\n+@UID89\n+NCGAGAATCCCTATTATTTTGTTGCTAAAAATTTAATAGATCGGAAGAGCACACGTCTGAACTCCAGTC\n++\n+#0<FFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIIIIIIIIIF\n+@UID90\n+NGCAGAATAATGTAATACCTCCAGATATGTAATTATTTGTAACAGATCGGAAGAGCACACGTCTGAACT\n++\n+#0<FFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@UID91\n+AAGCGGCGAGATCCCACTCCTGACACCATCGGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTC\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIFFIIIIIIIFFFFFFFFFFFFFFFFFFFFFFFFFFFB\n+@UID92\n+AAGTCACGGATCATGTGCGTCCCTCCCGAAGCTGCGCGCTCGGTCGTGCTAAGATCGGAAGAGCACACG\n++\n+BBBFFFFFFFFFFIIIIIIFIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFBFFFFBFFFFFFFF\n+@UID93\n+CATAGAATAATTGATAGATCGGAAGAGCACACGTCTTGTAGCAGATCGGAAGAGCACACGTCTGAACTC\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIIIIIIIFFFFFFF\n+@UID94\n+AATTCACGCAAAATAGAAGTCCTGATAGCCCAGACAACTGAGATCGGAAGAGCACACGTCTGAACTCCA\n++\n+BBBFFFFFFFFFFFFFFFFBFFIFFFFFFBBFFFFFIBFFBFFFFIFFFBBBFBFBFFBFFF<B<FFFF\n+@UID95\n+GCATCACGACTCATCCTCTATGGACATTGGAGTTTTTCATTATGTGCATGGATCAAGATCGGAAGAGCA\n++\n+BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIF\n+@UID96\n+NCAAGAATCACTGAATCCAGCGATCCGAGTTCTGTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTC\n++\n+#0<FFFFFFFFFFIIIIIIIIIIIIIIFIFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFF\n+@UID97\n+NCCAGAATCCTTTCACATGTATAAGGTGGCTCCATAGCTTACTGAGATCGGAAGACACACGTCTGAACT\n++\n+#0<FFFFFFFFFFIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIIFFIIIIIIIIIIIIIIIIIIIIIII\n+@UID98\n+CCAAGAATCCGCGTGGTGGCATGTGCCTGTGGTCCCAGATAGCAGATCGGAAGAGCACACGTCTGAACT\n++\n+BBBFFFFFFFFFFFIIFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFF\n+@UID99\n+TATCGGCGAGAACGCATAAATCTTTCGCCTTTTACTAAAGATTTGTGGCAGATCGGAAGAGCACACGTC\n++\n+BBBFFFFFFFFFFIIFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIFFFFFFFFBFFFBFFBFFFFF\n' |
| b |
| diff -r 000000000000 -r 0e70f9058b02 test-data/readswithtail.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/readswithtail.fastq Tue Nov 14 05:53:02 2017 -0500 |
| b |
| @@ -0,0 +1,8 @@ +@longenough +ACTAGAAT ++ +F0<FFFFF +@tooshort +GGTTAAC ++ +AAAFFFF |
| b |
| diff -r 000000000000 -r 0e70f9058b02 test-data/readswithtailremoved.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/readswithtailremoved.fastq Tue Nov 14 05:53:02 2017 -0500 |
| b |
| @@ -0,0 +1,8 @@ +@longenough +A ++ +F +@tooshort +N ++ +B |
| b |
| diff -r 000000000000 -r 0e70f9058b02 test-data/result_original_head.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result_original_head.fastq Tue Nov 14 05:53:02 2017 -0500 |
| b |
| b"@@ -0,0 +1,400 @@\n+@UID0\n+AGGAAAAATGTATGCTTGTGACCAATAAATATAAAAGGTTAAGATCGGAAGAGCACACGTCTG\n++\n+FFFFFFFFFIFIIIIIIIIIIIIIIFIIIIIIFIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@UID1\n+TACCAGTTGGTCCGAGTGTTGTGGGTTATTGTTAACTAAGATCGGAAGAGCACACGTCTGAAC\n++\n+FFFFFFFIIIIIIIFFFFFIIIIIIFIFIIIIIIIIIFFIFIIIIFFIIFFFFFFFFFFFBFB\n+@UID2\n+AGCCTTTTCCTTTGCCCTGATCTTGTCGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT\n++\n+<BFBFBFIFFFBFFFFFFFBBB0BBFFFBB<FB707'BFF0FFB'<B<BF#############\n+@UID3\n+TCTGGTTGGCGTTTGGTGTGTGGCTGTTTCTGCTCATTGATAGATCGGAAGAGCACACGTCTG\n++\n+FFFFFFFIIFFFFIIIFFFFFFIFIIFIIFFIFIIIFIIFFIIIIFIIFFFFFFFFFFFFBFF\n+@UID4\n+AGACTGCTTTAATTCTAAATAAAAATTTATTGCCAAGATCGGAAGAGCACACGTCTGAACTCC\n++\n+BFFFFFFIIIFFFIIIIIIFIIFIFFIFIIIIFFIIIIIIIIIIIBFFFIIIIIIIIFIIIFF\n+@UID5\n+AGGAATTGCCCCCCCCCACAACCGCGCTTGACTAGCGTAGCAGATCGGAAGAGCACACGTCTG\n++\n+FFFFFFFI0<FFFFIIIIIIIIIIIFBFFBFFFFBBFBFFFBBFFFFFFFFBBBFBFFFBBBB\n+@UID6\n+TCAAGTGTCCTCAGCAAAAGCTGGGTGGTTACCAAGATCGGAAGAGCACACGTCTGAACTCCA\n++\n+FFFFFFFFFFFIIIIIIFIFFIIIIBFFIIBBF<BFBFFFFIII7FFBFFFFBBBBBBFF<<B\n+@UID7\n+GACAATCCGAGTCACGGCACCATGTTAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTC\n++\n+FFFFFFFIIIIFIIIIIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFFB\n+@UID8\n+AGAATCTTCTTAGAGTTGGTTAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCATTCA\n++\n+FFFFFFFIFFIFI<FBFFFFFFIFFFFFFIBFBBFBFFFFFFFFFBBFFBB<7BFFF<<BB<B\n+@UID9\n+AGAAATTACTAAATGTGAAAAACATAATGTGAAAAGTATATGTTAAGATCGGAAGAGCACACG\n++\n+FFFFFFFIIIIFFIIFIFIFIIFIFFFFF<BFFFIFFFIIIIIIIFFFIFF<FIIIIIIFIFI\n+@UID10\n+AGGACCTGTAAACAGAATGATAAAGTATGTGATAGATCGGAAGAGCACACGTCTGAACTCCAG\n++\n+FFFFFFFIIIIIIIIIIIIIIIIIIFFIIFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@UID11\n+TCAATCTGGCATGTTGGAACAATGTAGGTAAGGGAAGTGGTCAAGATCGGAAGAGCACACGTC\n++\n+FFFFFFFIIIIIIIIIIIIIIIIIIIIIFFIIIIFIIFIIFIIIIIIIIIIIIIIIIIIFFFF\n+@UID12\n+AGGGTTAAAGTTGCTGGCCTAATGAGCTCAGTAGATCGGAAGAGCACACGTCTGAACTCCAGT\n++\n+FFFFFFFIIIIIIIIIIIIIFFIIIIIIIIIIIIIIIIIIIIIFFIIIIIIIIIFIIIIIIIF\n+@UID13\n+AGAAATCTTATTAATTCCCTCAAAAGCAGGTTAAGATCGGAAGAGCACACGTCTGAACTCCAG\n++\n+FFFFFFFIIIIIIIIIIIIIIIIIIIIIIIFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIF\n+@UID14\n+TCATGGTTGAGATCGGAAAGCACTATCGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT\n++\n+FFFFFFFIIIIIIIIIIIIIIIIFIIIIFIFIIIIIIIIIIIIIIIFFIFFFFFFFFFBFBFF\n+@UID15\n+AGCCGCCCACCCAGGGACGCCAGGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCA\n++\n+FFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFFFFFBFFFFFF\n+@UID16\n+CGCTATCCCACTTCTGACACCAGGCTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTC\n++\n+FFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFFFFFFFFFB\n+@UID17\n+CGGAGTCTGTTATAAAATGGACTTAACTGCCGAGATCGGAAGAGCACACGTCTGAACTCCAGT\n++\n+FFFFFFFIIIIIIIIIIIIIFIIIIIIIIIIIIFFFFFFFFFFFFFFFFFFFFFFFFFFFBFF\n+@UID18\n+AGCCGTCTAGAATGTAGCATCTAGTGACTTTTTAAAGCCGGTTAAGATCGGAAGAGCACACGT\n++\n+FFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFF\n+@UID19\n+TTTCCTGGGCATCCCGGGGATCCCAGAGCCGGCCCAGGTAGGCCAAGATCGGAAGAGCACACG\n++\n+FFFFFFFIIFIIIIIIFFFIIIIIIIIIIIFIIBFIIIBBFFFFBFFFFFFFFFBFFBFBFFF\n+@UID20\n+TCGGCCTACTCTACTTTCTGTTGCCGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCA\n++\n+FFFFFFFFIFIIIIIIIIIFFFFIIIIIIFFFIFF<FFFFFFF<<BFBFFFFFFFBBBBFFFB\n+@UID21\n+TCCAATCATGTTCGCCTCACACGCGAAAGGTCTTGACAGATCGGAAGAGCACACGTCTGAACT\n++\n+FFFFFFFIIIIIIIIIIIIIIIIIIIIIIIFFIIIIIIIIFFFFFFFFFFFFFFFFFFFFFFF\n+@UID22\n+CGCGACCTAATGTTAGTGAATATTACTAAGTTGCCAAGATCGGAAGAGCACACGTCTGAACTC\n++\n+FFFFFFFIIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFFFFFF\n+@UID23\n+TCGCGGTGGGATCCCGCGGCCACAGTAGATCGGGAGAGCACACGTCTGAACTCCAGTCACTCA\n++\n+FFFFFFBBFF0'BFF<B<B7B0<7<'<<7'7<<'0'7<7<<<7'0<<<<B'0<B'00<BB###\n+@UID24\n+TCCGACAGCCACAAGTTACATAGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCATT\n++\n+FFFFFFFIIIIIIIIFIIIIIIIIIIIIIIIIIIIIFIIIIIIIFFFFFFFFFFFFFFFFFFF\n+@UID25\n+GCACTCTCGTAGTTGGATCTTGGGAGCGGGCGGGCGGCTAAGATCGGAAGAGCACACGTCTGA\n++\n+FFFFBFFFFIIFFIFFFFFFFFFFFFFFFFBBF7BB7BFFBFBBBBBFB7BBFFFFBFB<BBB\n+@UID26\n+GACATGCACGCGTGGGTTCGTATCCCGATCAAGATCGGAAGAGCACACGTCTGAACTCCAGTC\n++\n+FFFFFFFIIIIIFFIIBFFFFFIIIIIIIIFFIIFFFFFFFFFFFFFFBFBBBBBBBBBBBBB\n+@UID27\n+AGCCATTTTTTCTTACTAGCTTGCAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTC\n++\n+FFBFFFFFFFFIIIIFFIFFBFFFFFFFIBBFFIFFFBFFFIFF<<BBBFFFFFIFFFFFFF<\n+@UID28\n+TCAATTCCCCGCGCAGGTTCGTATCCTGCCGACT"..b'IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFF\n+@UID72\n+GAAATTTCCAACAGCTTATCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCATTCAT\n++\n+FFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFIIIF\n+@UID73\n+CGCATCCCCGCGAGGGGCCCGGGGCTCAGCAGATCGTAATAGATCGGAAGAGCACACGTCTGA\n++\n+FFFFFFFIIIIIFFBFFFFFFFFFFFFFBFFFFFFFFFFFFFBBBFFBBBFBFFFBFFBBFBB\n+@UID74\n+TCGCATCCAGATTCTGTAGAGCTGGACAGGCAGGTGGTAGATCGGAAGAGCACACGTCTGAAC\n++\n+FFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIBFFFFFIIIIIIIFIIIIIIFFFFFFFFF\n+@UID75\n+AGCCTTAACATTTTATTATTTATTGTAAAATCAATTTGTGACAGATCGGAAGAGCACACGTCT\n++\n+FFFFFFFIIFFFIIIIIIFIIFFIIFFIIFBFF<FIBFBBBFB7BFFFB<FFIFIIFFFFIBF\n+@UID76\n+AGGATTTTAACCTGCAATTTGCCTCAGCAACAGGTTAAGATCGGAAGAGCACACGTCTGAACT\n++\n+FFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIIIIIIIIIIIIF\n+@UID77\n+TCGGCTCCTCCCCTTCGTCTTCACAGAGCTGGTCAAGATCGGAAGAGCACACGTCTGAACTCC\n++\n+FFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIIFFFFFFFFFFFFF\n+@UID78\n+AGGATTTATAACCACAACAAGAAGGGAATCAATGTTAAGATCGGAAGAGCACACGTCTGAACT\n++\n+FFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFF\n+@UID79\n+AGCAATGACCAATTACCAAGGAAGCTAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTC\n++\n+FFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFF\n+@UID80\n+AGCCTCACCCTAACACCCTTCAATACAATGTTTACAGGGTTAAGATCGGAAGAGCACACGTCT\n++\n+FFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFIIIIIIIIIIIIIIIIIIFFFF\n+@UID81\n+TCACTTTGTTAAGTTGATTTAACATTGCCCCCCCCACAACTTGGCAGATCGGAAGAGCACACG\n++\n+FFFFFFFIIIIIIFIIIIIIIIIIIFFFIIIIIIIIIFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@UID82\n+AGGATTTTAACTAAGGTGGTGACACTGGTAACAGATCGGAAGAGCACACGTCTGAACTCCAGT\n++\n+FFFFFFFIIIIIIIIIFFFFFFIIIIIIFFIIIIIIIIIIIFFFIIIIIFFFIIIIIIIIFFF\n+@UID83\n+AGAAAATAAGTGTGATCAATCTTTTTGTCGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA\n++\n+FFFFFFFIIIFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFF\n+@UID84\n+AGAATTTGACAACTTTAAATGAGTGTAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC\n++\n+FFFFFFFIIIIIIIFIIFIIIIIIIFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIF\n+@UID85\n+AGAAGTTATTCCTTTAAAAGAAATTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT\n++\n+BBFFFFBFFIFFFIFFFFFFBFFFFFIIFFFIFFIBFBBB<FFBBB<BFFFFB<BBFBBFFFB\n+@UID86\n+AGAAGCTAGAGCAGGCCTGCTTGCGGCTCCCTGTGGTTAAGATCGGAAGAGCACACGTTGAAC\n++\n+FFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIIIIIIIIIFFFFFFFFFFFFFF\n+@UID87\n+AGAACTTAAATTGATTAAAACTTTGTAGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC\n++\n+FFFFFFFIIIIIIIIIIIIIIIIIIFIIFIIIIIIIIIFIIIIIIIIIIIIFIIIIIIIIIIF\n+@UID88\n+AGCGATCTCGGTGGAACCTCCAGGTTAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTC\n++\n+FFFFFFFIIIIIIIIIIIIIIIIIFFIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFB\n+@UID89\n+AGCCCTATTATTTTGTTGCTAAAAATTTAATAGATCGGAAGAGCACACGTCTGAACTCCAGTC\n++\n+FFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIIIIIIIIIF\n+@UID90\n+AGAATGTAATACCTCCAGATATGTAATTATTTGTAACAGATCGGAAGAGCACACGTCTGAACT\n++\n+FFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@UID91\n+CGAGATCCCACTCCTGACACCATCGGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTC\n++\n+FFFFFFFIIIIIIIIIIIIIIIIIIIFFIIIIIIIFFFFFFFFFFFFFFFFFFFFFFFFFFFB\n+@UID92\n+TCGATCATGTGCGTCCCTCCCGAAGCTGCGCGCTCGGTCGTGCTAAGATCGGAAGAGCACACG\n++\n+FFFFFFFIIIIIIFIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFBFFFFBFFFFFFFF\n+@UID93\n+AGAATTGATAGATCGGAAGAGCACACGTCTTGTAGCAGATCGGAAGAGCACACGTCTGAACTC\n++\n+FFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIIIIIIIFFFFFFF\n+@UID94\n+TCCAAAATAGAAGTCCTGATAGCCCAGACAACTGAGATCGGAAGAGCACACGTCTGAACTCCA\n++\n+FFFFFFFFFFFFFBFFIFFFFFFBBFFFFFIBFFBFFFFIFFFBBBFBFBFFBFFF<B<FFFF\n+@UID95\n+TCACTCATCCTCTATGGACATTGGAGTTTTTCATTATGTGCATGGATCAAGATCGGAAGAGCA\n++\n+FFFFFFFIIIIIIIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIF\n+@UID96\n+AGCACTGAATCCAGCGATCCGAGTTCTGTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTC\n++\n+FFFFFFFIIIIIIIIIIIIIIFIFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFF\n+@UID97\n+AGCCTTTCACATGTATAAGGTGGCTCCATAGCTTACTGAGATCGGAAGACACACGTCTGAACT\n++\n+FFFFFFFIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIIFFIIIIIIIIIIIIIIIIIIIIIII\n+@UID98\n+AGCCGCGTGGTGGCATGTGCCTGTGGTCCCAGATAGCAGATCGGAAGAGCACACGTCTGAACT\n++\n+FFFFFFFFIIFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFF\n+@UID99\n+CGAGAACGCATAAATCTTTCGCCTTTTACTAAAGATTTGTGGCAGATCGGAAGAGCACACGTC\n++\n+FFFFFFFIIFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIFFFFFFFFBFFFBFFBFFFFF\n' |
| b |
| diff -r 000000000000 -r 0e70f9058b02 test-data/twomates.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/twomates.sam Tue Nov 14 05:53:02 2017 -0500 |
| b |
| @@ -0,0 +1,5 @@ +@HD VN:1.0 SO:unsorted +@SQ SN:chr1 LN:249250621 +@PG ID:bowtie2 PN:bowtie2 VN:2.2.0 CL:"/usr/local/user/bowtie2/bowtie2-2.2.0/bowtie2-align-s --wrapper basic-0 --very-sensitive --end-to-end --no-mixed --no-discordant --fr --omit-sec-seq --minins=0 --maxins=200 --threads 24 --time -x ../genome/hg19/hg19 --passthrough -1 /tmp/10410.inpipe1 -2 /tmp/10410.inpipe2" +39V34V1:167:HAWHUADXX:1:1101:19513:10724 99 chr1 45244081 40 41M = 45244081 -41 GTCCAGTTCTGCTACCGACAGTAAGTGAAGATAAAGTGTGT FFFIIIFIIIIIIFIIIIIIIFIIIBFFIIIIIIIIFFFFF AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T25 YS:i:-6 YT:Z:CP +39V34V1:167:HAWHUADXX:1:1101:19513:10724 147 chr1 45244081 40 41M = 45244081 -41 GTCCAGTTCTGCTACCGACAGTAAGTGAAGATAAAGTGTGT IFIIFIIIFIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFF AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T25 YS:i:-6 YT:Z:CP |
| b |
| diff -r 000000000000 -r 0e70f9058b02 test-data/tworeads_aln_ends.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tworeads_aln_ends.bed Tue Nov 14 05:53:02 2017 -0500 |
| b |
| @@ -0,0 +1,1 @@ +chr1 45244080 45244121 39V34V1:167:HAWHUADXX:1:1101:19513:10724 2 + |