mktrost

BamUtil Dedup requires 2 passes through the bam file, so as you discovered, does not work when reading from stdin. However there is definitely a bug in the implementation that...

I have updated the code and documentation for Dedup to specify that stdin is not supported. The code now produces an error message to let the user know. Let me...

Sorry, for the delayed response. I just got back from vacation traveling overseas. Yes, that is the correct place to make the modification. But in the code you included above...

There are two ways to solve this issue: 1) download the latest version of libStatGen, 2) make a few changes to the version of libStatGen that you have. 1) If...

Here is the reasoning behind the extra clips you see: Paired-end sequences from each end of a DNA fragment. Based on that, the start position of the forward strand corresponds...

The command seems to be missing the -lz at the end of the compile command. I think then it isn't pulling in the zlib information when compiling. I'm pretty sure...

You may not have C++11 (which includes unordered_map). If you want to compile without C++11, you can try one of the following: 1) Update bamUtil/Makefile.inc, line 7, change CXX11_AVAIL ?=...

You are correct, there was a getopt problem with that tool. I checked a fix into master. Please let me know if that resolves your problem. Thank you

Bam diff matches by name and fragment from the flag. In your case, do you have multiple reads in a single file that have the same name and fragment flag...

You are correct, the unordered_map requires a newer version of C++. The makefile attempts to detect your version and use a map if you don't have unordered_map, but this does...