[alito]

The code in savR doesn't seem to support version 6 from what I can see (https://github.com/Bioconductor-mirr...savR-methods.R) although it seems to support v5.

FWIW, here's the format for V6 (very similar to v5 as described in https://tracker.tgac.ac.uk/browse/MISO-138):


byte 0: file version number (6)
byte 1: length of each record
byte 2: quality score binning (byte flag representing if binning was on), if (byte 2 == 1) // quality score binning on
byte 3: number of quality score bins, B
bytes 4 - (4+B-1): lower boundary of quality score bins
bytes (4+B) - (4+2*B-1): upper boundary of quality score bins
bytes (4+2*B) - (4+3*B-1): remapped scores of quality score bins (QRemapped)
The remaining bytes are for the records, with each record in this format:
2 bytes: lane number (uint16)
2 bytes: tile number (uint16)
2 bytes: cycle number (uint16)
4 x B bytes: number of clusters assigned score (uint32) (QRemapped)


For the MiniSeq, B = 7.

[dpryan]

Here's the original github repository that people can make PRs against and issues for.

[ploverso-pgdx]

The code in savR doesn't seem to support version 6 from what I can see (https://github.com/Bioconductor-mirr...savR-methods.R) although it seems to support v5.

FWIW, here's the format for V6 (very similar to v5 as described in https://tracker.tgac.ac.uk/browse/MISO-138):


byte 0: file version number (6)
byte 1: length of each record
byte 2: quality score binning (byte flag representing if binning was on), if (byte 2 == 1) // quality score binning on
byte 3: number of quality score bins, B
bytes 4 - (4+B-1): lower boundary of quality score bins
bytes (4+B) - (4+2*B-1): upper boundary of quality score bins
bytes (4+2*B) - (4+3*B-1): remapped scores of quality score bins (QRemapped)
The remaining bytes are for the records, with each record in this format:
2 bytes: lane number (uint16)
2 bytes: tile number (uint16)
2 bytes: cycle number (uint16)
4 x B bytes: number of clusters assigned score (uint32) (QRemapped)


For the MiniSeq, B = 7.

SavR definitely supports version 6- I'm the one that wrote the code to support it. Here's the commit that added support: https://github.com/bcalder/savR/comm...506336250cec1c