| Previous changeset 0:2445d53549ba (2017-11-04) Next changeset 2:4070f129540a (2017-11-08) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 160b3085e5c9152fc8eaeb2e8afc12cdc1abe739 |
|
modified:
minimap2.xml test-data/minimap2-test1-fasta.bam test-data/minimap2-test1.bam test-data/minimap2-test2.bam |
| b |
| diff -r 2445d53549ba -r b103bc946f57 minimap2.xml --- a/minimap2.xml Sat Nov 04 05:41:11 2017 -0400 +++ b/minimap2.xml Wed Nov 08 10:02:24 2017 -0500 |
| b |
| @@ -1,8 +1,8 @@ <?xml version="1.0"?> -<tool id="minimap2" name="Map with minimap2" version="2.3" profile="17.01"> +<tool id="minimap2" name="Map with minimap2" version="2.4" profile="17.01"> <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description> <requirements> - <requirement type="package" version="2.3">minimap2</requirement> + <requirement type="package" version="2.4">minimap2</requirement> <requirement type="package" version="1.6">samtools</requirement> </requirements> <version_command>minimap2 --version</version_command> @@ -429,14 +429,12 @@ recent samtools will throw an error and abort. Older samtools and other tools may create corrupted BAM. -To avoid this issue, you can add option ``-L`` at the minimap2 command -line. This option moves a long CIGAR to the ``CG`` tag and leaves a -fully clipped CIGAR at the SAM CIGAR column. Current tools that don’t -read CIGAR (e.g. merging and sorting) still work with such BAM records; -tools that read CIGAR will effectively ignore these records. I have pull -requests to the SAM spec, htslib, htsjdk, bedtools2, Rsamtools and -igv.js. If they are accepted, future versions of these tools will -seamlessly recognize long-cigar records generated by option ``-L``. +To avoid this issue, you can add option ``-L`` at the minimap2 command line. +This option moves a long CIGAR to the ``CG`` tag and leaves a fully clipped +CIGAR at the SAM CIGAR column. Current tools that don’t read CIGAR +(e.g. merging and sorting) still work with such BAM records; tools that read +CIGAR will effectively ignore these records. It has been decided that future +tools will seamlessly recognize long-cigar records generated by option `-L`. **TD;DR**: if you work with ultra-long reads and use tools that only process BAM files, please add option ``-L``. |
| b |
| diff -r 2445d53549ba -r b103bc946f57 test-data/minimap2-test1-fasta.bam |
| b |
| Binary file test-data/minimap2-test1-fasta.bam has changed |
| b |
| diff -r 2445d53549ba -r b103bc946f57 test-data/minimap2-test1.bam |
| b |
| Binary file test-data/minimap2-test1.bam has changed |
| b |
| diff -r 2445d53549ba -r b103bc946f57 test-data/minimap2-test2.bam |
| b |
| Binary file test-data/minimap2-test2.bam has changed |