Add an IntervalCodec that use useful for sorting large sets of #1288
Conversation
Codecov Report
@@ Coverage Diff @@
## master #1288 +/- ##
===============================================
+ Coverage 67.495% 67.587% +0.092%
- Complexity 8150 8178 +28
===============================================
Files 558 561 +3
Lines 33364 33409 +45
Branches 5608 5611 +3
===============================================
+ Hits 22519 22580 +61
+ Misses 8657 8641 -16
Partials 2188 2188
|
|
I may need to also make a |
There was a problem hiding this comment.
@nh13 Thank you, this seems useful. I have two very minor comments and then it's good to merge 👍
This may be useful when writing intervals to a file when storing all the intervals in memory is not possible.
nh13
force-pushed
the
nh_interval_codec
branch
from
38fa596
to
bd872b5
Compare
|
@lbergelson commit bd872b5 is needed for this PR to be fully useful for the PR in Picard. Thanks for the review! |
There was a problem hiding this comment.
@nh13 A few more comments on the new changes. 👍 when they're resolved.
|
|
||
| // Write out the intervals | ||
| try { | ||
| final IntervalListWriter writer = new IntervalListWriter(file, this.header); |
There was a problem hiding this comment.
The common refrain, why not use a try-with-resources to autoclose this thing?
| /** Creates a new writer, writing a header to the file. | ||
| * @param file a file to write to. If exists it will be overwritten. | ||
| */ | ||
| public IntervalListWriter(final File file) { |
There was a problem hiding this comment.
Since this is now top new level code can you convert it use Path instead of File.
| public class IntervalListWriter implements Closeable { | ||
|
|
||
| private final BufferedWriter out; | ||
| private final FormatUtil format = new FormatUtil(); |
There was a problem hiding this comment.
I know this is just moving existing code, but this use of FormatUtil seems unnecessary. Wouldn't Integer.toString() serve the same purpose with less overhead?
|
|
||
| final IntervalList actualList = IntervalList.fromFile(tempFile); | ||
|
|
||
| Assert.assertEquals( |
There was a problem hiding this comment.
This should assert that the header is correct as well.
| return retval; | ||
| } | ||
| } | ||
| } |
There was a problem hiding this comment.
I think there's an extra }. It's not compiling.
nh13
force-pushed
the
nh_interval_codec
branch
from
e34d33f
to
7bbe157
Compare
There was a problem hiding this comment.
@nh13 Thanks. Going to merge this and then follow up with a pr that fixes the path issue.
| public IntervalListWriter(final File file, final SAMFileHeader header) { | ||
| out = IOUtil.openFileForBufferedWriting(file); | ||
| public IntervalListWriter(final Path path, final SAMFileHeader header) { | ||
| out = IOUtil.openFileForBufferedWriting(path.toFile()); |
intervals.
Description
This will be useful for using with a
SortingCollectionwhen we are sorting over MANY intervals. My intention is to submit a PR to Picard to use this codec andSortingCollectionwhen lifting over an interval list, as I sometimes run out of memory withLiftoverIntervalListeven with 32GB of memory.Checklist