search

mozack / abra

Assembly Based ReAligner
MIT License
70 stars 12 forks source link

SAM Read name length exceeded #1

Closed jstjohn closed 10 years ago

jstjohn commented 10 years ago

Hello, I am working with version 0.69 from the download page released about a month ago. I am running up against a lot of these warnings:

Warning!  Max SAM Read name length exceeded for: HWI-D00291:44:H8934ADXX:1:1113:19955:94195     177     chr1    91448912        16      67S23M11S       chr14   70252830        0       *       *       SA:Z:chr2,65392795,+,52S19M30S,0,0;chr3,180631113,+,38S19M44S,0,0;chr11,49594709,+,19M82S,0,0;chr2,177387370,-,54S19M28S,0,0;   PG:Z:MarkDuplicates     RG:Z:413.14     NM:i:0  YR:i:1  AS:i:23 XS:i:0  YX:i:58

Digging into the code I see this stuff happens around line 183 in both the latest checkout, and my version 0.69 of the file main/java/abra/Sam2Fastq.java.

It seems like there could be weirdness going on, because that variable is labeled as readName on line 195, yet it is printed out as what looks like a sam record.

Is all of this expected/ok/alpha version stuff, or is there a bug here?

Thanks for your time!

mozack commented 10 years ago

Hi John,

That's expected and it is safe to ignore that message. I'm writing way to much to the log file at the moment. Will try to get it cleaned up in the near future. Please do let me know if you run into any other issues.