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BamUtil: polishBam

3,542 bytes added, 15:21, 1 November 2010
no edit summary
Returns 0.
=== Example Output ===Command:
<pre>
../../bin/polishBam --in testFiles/sortedSam.sam --out results/updatedSam.sam --log results/updated.log --checkSQ --fasta testFiles/testFasta.fa --AS my37 --UR testFasta.fa --RG "@RG ID:UM0037:1 SM:Sample2 LB:lb2 PU:mypu CN:UMCORE DT:2010-11-01 PL:ILLUMINA" --PG "@PG ID:polish VN:0.0.1" --SP new --HD "@HD VN:1.0 SO:coordinate GO:none"
</pre>
 
Input File:
<pre>
@SQ SN:1 LN:2004
@SQ SN:2 LN:2000
@SQ SN:3 LN:2005
@SQ SN:4 LN:2040
@SQ SN:5 LN:2006
@RG ID:myID LB:library SM:sample
@RG ID:myID2 SM:sample2 LB:library2
@CO Comment 1
@CO Comment 2
18:462+29M5I3M:F:295 97 1 75 0 5M 18 757 0 ACGTN ;>>>> AM:i:0 MD:Z:30A0C5 NM:i:2 XT:A:R
18:462+29M5I3M:F:295 97 1 75 0 * 18 757 0 * * AM:i:0
1:1011:F:255+17M15D20M 73 1 1011 0 5M2D = 1011 0 CCGAA 6>6+4 AM:i:0 MD:Z:37 NM:i:0 XT:A:R
1:1011:F:255+17M15D20M 133 1 1012 0 * = 1011 0 CTGT >>9>
18:462+29M5I3M:F:296 97 1 1751 0 3S2H5M 18 757 0 TGCACGTN 453;>>>>
18:462+29M5I3M:F:295 97 2 75 0 5M 18 757 0 ACGTN * AM:i:0 MD:Z:30A0C5 NM:i:2 XT:A:R
18:462+29M5I3M:F:297 97 2 1751 0 3S5M1S3H 18 757 0 TGCACGTNG 453;>>>>5
18:462+29M5I3M:F:298 97 3 75 0 3S5M4H 18 757 0 TGCACGTN 453;>>>>
Y:16597235+13M13I11M:F:181 141 * 0 0 * * 0 0 AACT ==;;
Y:16597235+13M13I11M:F:181 141 * 0 0 * * 0 0 * *
</pre>
 
 
Output File:
<pre>
@SQ SN:1 LN:2004 AS:my37 M5:a9cfe5b8c11aa0cc2c0d2bf3602c9804 UR:testFasta.fa SP:new
@SQ SN:2 LN:2000 AS:my37 M5:7c342606b54aa211a50f5f63ac1cb2eb UR:testFasta.fa SP:new
@SQ SN:3 LN:2005 AS:my37 M5:c30e547093f33de240b164a4a2ebe3b5 UR:testFasta.fa SP:new
@SQ SN:4 LN:2040 AS:my37 M5:fc4c559e9da51e93e7875031ddf65f2a UR:testFasta.fa SP:new
@SQ SN:5 LN:2006 AS:my37 M5:c876194283debb8b507ebd0f82309ec4 UR:testFasta.fa SP:new
@RG ID:myID LB:library SM:sample
@RG ID:myID2 SM:sample2 LB:library2
@HD VN:1.0 SO:coordinate GO:none
@RG ID:UM0037:1 SM:Sample2 LB:lb2 PU:mypu CN:UMCORE DT:2010-11-01 PL:ILLUMINA
@PG ID:polish VN:0.0.1
@CO Comment 1
@CO Comment 2
18:462+29M5I3M:F:295 97 1 75 0 5M 18 757 0 ACGTN ;>>>> AM:i:0 MD:Z:30A0C5 NM:i:2 RG:Z:UM0037:1 XT:A:R
18:462+29M5I3M:F:295 97 1 75 0 * 18 757 0 * * AM:i:0 RG:Z:UM0037:1
1:1011:F:255+17M15D20M 73 1 1011 0 5M2D = 1011 0 CCGAA 6>6+4 AM:i:0 MD:Z:37 NM:i:0 RG:Z:UM0037:1 XT:A:R
1:1011:F:255+17M15D20M 133 1 1012 0 * = 1011 0 CTGT >>9> RG:Z:UM0037:1
18:462+29M5I3M:F:296 97 1 1751 0 3S2H5M 18 757 0 TGCACGTN 453;>>>> RG:Z:UM0037:1
18:462+29M5I3M:F:295 97 2 75 0 5M 18 757 0 ACGTN * AM:i:0 MD:Z:30A0C5 NM:i:2 RG:Z:UM0037:1 XT:A:R
18:462+29M5I3M:F:297 97 2 1751 0 3S5M1S3H 18 757 0 TGCACGTNG 453;>>>>5 RG:Z:UM0037:1
18:462+29M5I3M:F:298 97 3 75 0 3S5M4H 18 757 0 TGCACGTN 453;>>>> RG:Z:UM0037:1
Y:16597235+13M13I11M:F:181 141 * 0 0 * * 0 0 AACT ==;; RG:Z:UM0037:1
Y:16597235+13M13I11M:F:181 141 * 0 0 * * 0 0 * * RG:Z:UM0037:1
</pre>
 
Output:
<pre>
in testFiles/sortedSam.sam
out results/updatedSam.sam
log results/updated.log
checkSQ
</pre>
 
Log File:
<pre>
Arguments in effect:
--in [testFiles/sortedSam.sam]
--out [results/updatedSam.sam]
--log [results/updated.log]
--fasta [testFiles/testFasta.fa]
--AS [my37]
--UR [testFasta.fa]
--SP [new]
--checkSQ [ON]
--HD [@HD VN:1.0 SO:coordinate GO:none]
--RG [@RG ID:UM0037:1 SM:Sample2 LB:lb2 PU:mypu CN:UMCORE DT:2010-11-01 PL:ILLUMINA]
--PG [@PG ID:polish VN:0.0.1]
Reading the reference file testFiles/testFasta.fa
Finished reading the reference file testFiles/testFasta.fa
Finished checking the consistency of SQ tags
Creating the header of new output file
Adding 1 HD, 1 RG, and 1 PG headers
Finished writing output headers
Writing output BAM file
Successfully written 10 records
</pre>

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