MosaikSort

[koppk]

Hi Wan-Ping Lee,

after downloading Version 2.2.30 I got the buffer overflow error as mentioned in #11 when I tried to run the demo data. So as recommended there, I used version 2.2.26 and demo wun through without errors. However, when trying to visualize the output with Gambit entering the input files

demo/fastq/read.mka.bam and
demo/reference/e.coli.dat and creating a new index for each,

Gambit shut down throwing the error:
BAM file not properly sorted:
Alignment ecoli.000000001 : 4778334 > 2273411 on reference (id = 0)

So I looked up MosaikSort in the manual but couln't find it in src or bin.
Though plenty of
find -name ort
./obj/SortThread.o
./obj/SortNMergeUtilities.o
./obj/ArchiveSort.o
./obj/TimeSupport.o
./src/CommonSource/Utilities/TimeSupport.h
./src/CommonSource/Utilities/ArchiveSort.cpp
./src/CommonSource/Utilities/ArchiveSort.h
./src/CommonSource/Utilities/LargeFileSupport.h
./src/CommonSource/Utilities/SortThread.h
./src/CommonSource/Utilities/SortNMergeUtilities.cpp
./src/CommonSource/Utilities/SortThread.cpp
./src/CommonSource/Utilities/TimeSupport.cpp
./src/CommonSource/Utilities/SortNMergeUtilities.h

Or should I chnage to another visualization and which one do you recommend?

Any advice highly appreciated.
Thanks,
Katharina

[jotete]

Hi Katharina,

have you found a solution for your problem? I have the same issue here.

Best regards,
Joana