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NGS Aligner port from HPG Aligner #8

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imedina opened this issue May 18, 2015 · 0 comments
Open

NGS Aligner port from HPG Aligner #8

imedina opened this issue May 18, 2015 · 0 comments
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@jtarraga
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v0.6.0

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@imedina
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imedina commented May 18, 2015

Currently there is not am official NGS Aligner implemented for Hadoop although this has been discussed many times. Some initial tests using JNI have shown very good results.
@imedina imedina added the task label May 18, 2015
@imedina imedina added this to the v0.6.0 milestone May 18, 2015
jtarraga added a commit that referenced this issue May 28, 2015
@jtarraga
aligner: create file/folder structure to the hpg-aligner and add the …
21dc109 
…jni functions. #8
jtarraga added a commit that referenced this issue May 28, 2015
@jtarraga
align: create command line to align FastQ. #8
7d7a37d
jtarraga added a commit that referenced this issue May 28, 2015
@jtarraga
align: include the first version of the mapreduce job: ReadAlignMR. #8
468c44d
jtarraga added a commit that referenced this issue May 29, 2015
@jtarraga
align: simulate native map function returning SAM lines. #8
bc5cd80
jtarraga added a commit that referenced this issue May 29, 2015
@jtarraga
align: remove the function reducer in ReadAlignMR, and save the resul…
1aee2f1 
…t using the BAM/SAM Avro schema. #8
jtarraga added a commit that referenced this issue May 29, 2015
@jtarraga
align: add ReadAlignmentAlignMR function (prototype to re-map BAM fil…
457a40c 
…es following the ReadAlignMR mapreduce job) #8
jtarraga added a commit that referenced this issue Jun 1, 2015
@jtarraga
align: pass the class AlignerUtils from Java to C (prototype) #8
9e38f84
jtarraga added a commit that referenced this issue Jun 1, 2015
@jtarraga
align: build the dynamic library for hpg-aligner (not finished yet). #8
ab1d8ea
jtarraga added a commit that referenced this issue Jun 2, 2015
@jtarraga
align: build the dynamic library for hpg-aligner and fix build.sh. #8
4f43427
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