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cljam.io.bam-index.writer


*alignments-partition-size*clj

The number of alignments that is loaded each indexing process. This has an effect on performance of concurrent indexing. The default value is 10,000.

The number of alignments that is loaded each indexing process. This has an
effect on performance of concurrent indexing. The default value is 10,000.
sourceraw docstring

finalize-indexclj

(finalize-index nrefs index)

Converts intermediate BAM index data structure into final one. Must be called in the final stage.

Converts intermediate BAM index data structure into final one. Must be called
in the final stage.
sourceraw docstring

IndexStatusclj

source

make-index*clj

(make-index* alns)

Calculates index from the references and alignments, returning it as a map. Returned index is still intermediate. It must be passed to finalize function in the final stage.

Calculates index from the references and alignments, returning it as a map.
Returned index is still intermediate. It must be passed to finalize function
in the final stage.
sourceraw docstring

make-index-from-blocksclj

(make-index-from-blocks nrefs blocks)

Calculates a BAM index from provided references and alignment blocks. Optionally, you can do this process concurrently.

Calculates a BAM index from provided references and alignment blocks.
Optionally, you can do this process concurrently.
sourceraw docstring

merge-indexclj

(merge-index idx1 idx2)

Merges two intermediate indices, returning the merged intermediate index.

Merges two intermediate indices, returning the merged intermediate index.
sourceraw docstring

MetaDataclj

source

update-last-pointerclj

(update-last-pointer index eof-ptr)

Update the last pointer of the index to the given value.

Update the last pointer of the index to the given value.
sourceraw docstring

write-index!clj

(write-index! wtr alns)

Calculates a BAM index from alns, writing the index to a file.

Calculates a BAM index from alns, writing the index to a file.
sourceraw docstring

write-index*!clj

(write-index*! wtr nrefs indices)

Write the index to a file.

Write the index to a file.
sourceraw docstring

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