organize or remove irrelevant files from Download Files panel

[GoogleCodeExporter]

I think there are way too many irrelevant files on the Download File page, and 
it should be organized a little better or cleaned.  Probably the simplest way 
to organize would be to add new "Advanced File" headings that appear at the 
very bottom of the page.  Below are my suggestiosn for an organization, charlie 
may have modifications later.  the last one (008) could be omitted altogether 
for normal users.  

I also added some descriptions which could be used for tool tips.  

Note, i wasn't very careful with my regular expressions, so please double check.

---

001. Unaligned fastq files
s_*_sequence.txt : It would be nice if we added the LIMS id to these filenames 
as well.

002. Primary BAM Alignment Files
*%GENOME%.fa.mdups.bam[.bai]? : Main BAM file we want people to use

003. Base quality recalibrated BAM files
*realign.mdups.recal.ba[mi] : Recalibrated by Bis-SNP

004. Visualization tracks
*.BinDepths.metric.wig.bw : Read coverage in all genomic bins of "winsize" base 
pairs (UCSC bigwig file)
*.BinDepths.metric.wig : Read coverage in all genomic bins of "winsize" base 
pairs (UCSC bigwig file)
*CG.ct_coverage.tdf : Bis-SNP coverage track
*CG.tdf : Bis-SNP methylation track

005. Methylation tracks (Bisulfite-seq)
*CG.6plus2.bed : Bis-SNP methylation calls
*cpg.raw.sort.vcf : Bis-SNP methylation calls plus SNPs

006. Advanced Files, Alternate BAM Alignments
*NC_001416.fa.*bam* : Lambda control alignments (QC only)

007. Advanced Files, QC
nmerCount_* : Overrepresented oligomers
*_adapterTrim.csv
*%GENOME%*.mdups.bam.flagstat.metric.txt: Raw output from SAMTOOLS flagstat
*.CollectAlignmentSummaryMetrics.metric.txt : Raw output from Picard
*.CollectGcBiasMetrics.metric.txt : Raw output from Picard
*.CollectInsertSizeMetrics.metric.txt : Raw output from Picard

008. Intermediate internal pipeline files (not for general use)
*%GENOME%.fa.bam[.bai]? : This file is before mdups addition, shouldn't be 
needed
*_Gerald_mononucleotide.csv : By-product of QC metric computation
ContamCheck.* : By-product of QC metric computation
*_qcmetrics.csv : By-product of QC metric computation
*MethLevelAverages.metric.txt : By-product of QC metric computation
*%GENOME%*.bam.flagstat.metric.txt : Based on Pre-mdups BAM.  Not useful
*.NC_001416*flagstat.metric.txt : Lambda flagstat, By-product of QC metric 
computation
*InvertedReadPairDups.metric.txt : By-product of QC metric computation
*ReadLength.metric.txt : By-product of QC metric computation
*.ApplicationStackMetrics.metric.txt : By-product of QC metric computation
*.CPGvsRandomCov.metric.txt : By-product of QC metric computation
*.MeanQualityByCycle.metric.txt : By-product of QC metric computation
*.QualityScoreDistribution.metric.txt : By-product of QC metric computation
*DownsampleDups* : By-product of QC metric computation

Original issue reported on code.google.com by benb...@gmail.com on 17 Jan 2013 at 6:00

[GoogleCodeExporter]

Original comment by natalia....@gmail.com on 21 Feb 2013 at 9:19

• Changed state: Testing

[GoogleCodeExporter]

considering this fixed as of eccpgxt-beta

Original comment by zack...@gmail.com on 3 Apr 2013 at 11:24

• Changed state: Done