Comments (4)
My PR in htsjdk will not include an interface, but a FastqCodec
for easy conversion of SAMRecord
to FastqRecord
(better for implementation of our writers) and new methods for FastqRecord
for obtain the quality scores and bases (better for get rid of some unclear code).
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Probably this would be not done after #36
from readtools.
Supporting solexa qualities is a different issue (#62)
from readtools.
This is not going to happen, but the HTSJDK PR was accepted and the new functionality changes tracked in #138
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Related Issues (20)
- Start publishing ReadTools versions in maven central HOT 3
- Move javadoc documentation to a service (or gh-pages branch) HOT 1
- Migrate docs to its own repository (or gh-pages branch)
- Decide new theme or create one for help pages
- ReadsToDistmap: do not require maxReadLength HOT 2
- AssignReadGroupByBarcode: problem with doubly-barcoded reads HOT 6
- ReadsToDistmap: dump sam header somewhere (feature request) HOT 4
- DownloadDistmapResult: merge SAM header (feature request) HOT 3
- Support mixed dual/single indexed files in AssignReadGroupByBarcode HOT 9
- Better error message for malformed header in barcode file
- Add stacktrace to unexpected errors
- Create a way to identify issues for beginners/newcomers
- Better support for read groups in distmap integration HOT 1
- Specify that the property for default barcode separator is a regexp HOT 1
- Default barcode separators should be treated separately for split HOT 2
- DownloadDistmapResult fails with many parts HOT 1
- GemMappabilityToBed has problems with some invalid characters in mappability files HOT 1
- spurious assignment of read groups by barcodes with '+' delimiter HOT 7
- How to extract the UMI info in illumina read's name into a seperate tag HOT 1
- TrimReads for popoolation error
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