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note about travis integration
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slowkow committed May 29, 2015
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18 changes: 11 additions & 7 deletions CHANGELOG.md
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- refFlat

- This creates a file for the REF_FLAT argument of
CollectRnaSeqMetrics.
CollectRnaSeqMetrics.

- rRNA

- This creates a file for the RIBOSOMAL_INTERVALS argument of
CollectRnaSeqMetrics.
CollectRnaSeqMetrics.

- Travis continuous integration testing. Each time I push new changes to the
repo, Travis will automatically check that the picardmetrics output is
correct.

## Fixed

- This was harmless, but some of the collated output files were missing the
trailing tab character at the end of the line. Some also had extra lines
trailing tab character at the end of the line. Some also had extra lines
without data. Now all of the collated output files should be perfectly
formatted.

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## Changed

- `picardmetrics run` now puts the newly generated BAM file in `/tmp` and
deletes it after successfully running, unless the `-k` option is used.
deletes it after successfully running, unless the `-k` option is used.

- `picardmetrics run` now runs CreateSequenceDictionary and ReorderSam on
the BAM file to avoid issues where the sequence names in the header of the
BAM file is not in the same order as the sequence names in the reference
sequence FASTA file.

- Shuffled the header for `data/project1/sample2.bam` so we can ensure that
BAM files with unordered headers work correctly.
BAM files with unordered headers work correctly.

- Rearranged output files so you can see the extra metrics contributed by
CollectRnaSeqMetrics:
CollectRnaSeqMetrics:

- Compare the files in `out/default` with `out/rnaseq`.
- Compare the files in `out/default` with `out/rnaseq`.

## Removed

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