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Support for ALT-aware mapping #11

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jtarraga opened this issue Jan 26, 2015 · 0 comments
Open

Support for ALT-aware mapping #11

jtarraga opened this issue Jan 26, 2015 · 0 comments
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@jtarraga
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enhancement
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v2.1.0

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HPG Aligner has to take into account the ALT contigs: alternate haplotypes sequences for some chromosomes. The genome reference GRCh38 includes 261 ALT contigs, but this will become worse when more ALT contigs were added in the future.
@jtarraga jtarraga self-assigned this Jan 26, 2015
@jtarraga jtarraga added this to the v2.1.0 milestone Jan 26, 2015
jtarraga added a commit that referenced this issue Jan 28, 2015
@jtarraga
Adds support to create the SA index taking into account the ALT seque…
2b770bb 
…nces (#11)
jtarraga added a commit that referenced this issue Jan 29, 2015
@jtarraga
Fixes segmentation fault when building SA index (#11), and improves t…
59e9ba3 
…he help display for build index commands
jtarraga added a commit that referenced this issue Feb 2, 2015
@jtarraga
Creates SA index (of a genome with ALTs) and with a decoy genome with…
9c3117c 
…out merging genomes in a temporary file (#11)
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