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67 issues in ExpressionAnalysis/ea-utils

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#67

installing and building fastq-join on a linux server.

Hello, I am new to the command line and would appreciate help getting started with fastq-join. Can anyone give direction for how to install and build ea-utils on a linux server once the files have been ...

  • Opened by tbipf Jul 13, 2017
  • 5 comments
#66

int type overflow

#65

fix int type overflow

We got a couple of bugs in fastq-multx, and fastq-stats because some variable defined as int can't hold the total numbers generated by NovaSeq 6000. Change those variables' type to uint64_t to ...

#64

Avoid divide by zero in average length, std

One of the tests fails on some systems because of a divide-by-zero for one of the test datafiles. This fixes that test on those systems.

#63

Test for EOF at beginning of file--exit gracefully

Allows merging of empty files without exiting with status 1.

#62

The total count of sequences is overflow

As int type, which is 32-bit signed integer, the largest number is 2147483648, but NovaSeq 6000 has about 5,000,000,000 seuences. Change the total, and the count for each barcode to uint64_t, which is ...

#61

number overflow

Many variables are defined as int, which can hold up to maximal about 2,000,000,000. The latest assays might have more than 5,000,000,000 sequences count. There are needs to inspect code, and change variables ...

#60

fastq-multx not identifying barcodes

I have a fastq file with 1.7 million reads of 75 bps, and 28 different barcodes. My command: ``fastq-multx -l barcodes.txt all_samples.fastq -e -o %.fq -x" Part of my barcode file: barcodes.txt: ...

  • Opened by SJRussell May 10, 2017
  • 5 comments
#59

No output when running fastq-mcf

Hello. An error arises when I was running fastq-mcf. Here is my command to run the program. ~/local/bin/fastq-mcf /dev/null ./test1.fastq.gz -o ea1.fq -0 -R --qual-mean 20 -s 0 -l 33 -n And the stdout ...

#58

new dockerfile

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