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Text Only Genome Viewer!

Home Page: http://asciigenome.readthedocs.io/en/latest/description.html

License: MIT License

Shell 0.04% Java 98.73% Ruby 0.04% Awk 0.39% Python 0.79%

genome-viewer terminal command-line

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asciigenome's Issues

awk incompatible with next and find

Setting the awk filter prevents next and find to move to features outside the current window. This is because the awk filter stores a set of intervals (in field IntervalFeatureTrack.awkFiltered) which are considered valid.

Reproduce:

ASCIIGenome -x 'bookmark && +1k && bookmark && +1k && bookmark && 1'
awk '$4 > -1'  <- do not filter anything,  always true.
next <- does not move!
awk <- remove filter
next <- now it does move

Solutions? Maybe instead of storing the set of features passing filter, store the awk script itself. Every time the method featureIsVisible is computed, re-run the awk script and filter accordingly (this is quite expensive of course).

Adding bams from different genomes

If you try to load bam files aligned to different genomes you get a rather misleading message:

ASCIIGenome fk045_hyd1.Lmaj.bam fk068_Ldono_fU1.ldon.bam
Initializing coordinates... 
Unable to classify fk068_Ldono_fU1.ldon.bam; skipping <---

Here fk045_hyd1.Lmaj.bam is Leishmania major genome and fk068_Ldono_fU1.ldon.bam is L. donovani so it's fine to drop fk068 as chromosomes don't match. The message (Unable to classify) however is misleading

Error with `seqRegex ^`

Searching for seqRegex ^ gives:

Invalid coordinates: 1 0
Exception in thread "main" java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Caused by: exceptions.InvalidGenomicCoordsException
    at tracks.IntervalFeature.validateIntervalFeature(IntervalFeature.java:190)
    at tracks.IntervalFeature.intervalFeatureFromBedLine(IntervalFeature.java:139)
    at tracks.IntervalFeature.<init>(IntervalFeature.java:57)
    at samTextViewer.GenomicCoords.findRegex(GenomicCoords.java:757)
    at samTextViewer.Main.main(Main.java:299)
    ... 5 more

Exception handling on missing bam index

If a an input bam file doesn't have an index, you get a horrible stack trace. Fix it by giving a more gentle message.

Load plain wig format

Files in plain wig format are not handled correctly (bigWig ok). To load wig files you probably need to have the correct genome set since this is necessary to convert wig to bigWig. In the meantime one can use wigToBigWig from UCSC utils:

wigToBigWig in.wig chrom.sizes out.bw

Print features puts omitted in the wrong place

When printing more features than set by print -n xxx, the string [n/m features omitted] is printed above everything and it's not very useful.

trim with window resizing

trim doesn't play very well with terminal window resizing try:

ASCIIGenome hg19_genes_head.gtf.gz -r chr1:11583-12359

Then execute trim -> ok. Then resize terminal window to make it smaller, trim again. You get:

java.lang.IndexOutOfBoundsException: Index: 85, Size: 85
	at java.util.ArrayList.rangeCheck(ArrayList.java:653)
	at java.util.ArrayList.set(ArrayList.java:444)
	at tracks.TrackIntervalFeature.printToScreenOneLine(TrackIntervalFeature.java:361)
	at tracks.TrackIntervalFeature.printToScreen(TrackIntervalFeature.java:312)
	at samTextViewer.TrackProcessor.iterateTracks(TrackProcessor.java:66)
	at samTextViewer.InteractiveInput.processInput(InteractiveInput.java:325)
	at samTextViewer.Main.main(Main.java:156)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)

~~Then resize window again to make it larger. zoom out and go to another feature. trim again. the window has become smaller.~~

You probably need to play with getUserWindowSize() in the trim method.

There are other issues with trim. Make this method undocumented for now

Add colours to png output

Methods ansiForegroundColourToGraphicsColor(int ansiColor) and Color ansiBackgroundColourToGraphicsColor(int ansiColor) in coloring.ColorChar.java do not list all the colours available on screen (e.g. magenta, cyan). Add them.

brew installation

It would be good to have a brew formula, to install Asciigenome more easily.

(I've already written it, I'll send a push request to linuxbrew in a few minutes)

`next` returns chunks of fasta sequence

There is a bug in v0.2.0 where in some cases calling next incorrectly print chunks of fasta sequence (if fasta file is available). This is because the method GenomicCoords.centerAndExtendGenomicCoords() changes the coordinates of the GenomicCoords object but it doesn't update the underlying sequence.

This has been fixed in forthcoming v0.3.0 where refseq is no loger an attribute of GenomicCoords. Now the sequence is extracted it fresh from the fasta file using the current coordinates and this gives you an up-to-date sequence.

addTracks with regex

addTracks should expand wild card characters, e.g. addTracks peaks/hela*.narrowPeak

Rename tmp file for TrackIntervalFeature

When reading a plain bed file, the bgzip'd file and index have name *.bed and .*.bed.tbi. Change it to be *.bed.gz. It makes no difference but better to be consistent.

`next` command messes up track IDs

Load a non intervalFeature file and an interval file:

ASCIIGenome -x 'next' -ni -nf test_data/ear045.oxBS.actb.tdf test_data/hg19_genes_head.gtf

These will have IDs #1 and #2. Now issue the next command. The second file gets renamed to have ID #1!

`extend` should understand k and m suffixes

This should be enabled:

extend 10k
extend 10m

Remote tabix index is not used

Version 0.6.4: It appears remote tabix files are first downloaded locally. I.e. the remote tabix index is not used!

As shown by infoTracks, the working file is a local one:

ASCIIGenome
addTracks ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/input_call_sets/ALL.wex.union_illumina_wcmc_bcm_bc_bi.20110521.snps.exome.sites.vcf.gz
infoTracks

infoTracks 
------
Track tag:    ALL.wex.union_illumina_wcmc_bcm_bc_bi.20110521.snps.exome.sites.vcf.gz#1
Input source: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/input_call_sets/ALL.wex.union_illumina_wcmc_bcm_bc_bi.20110521.snps.exome.sites.vcf.gz
Working file: /tmp/asciigenome.5141873215838905009.ALL.wex.union_illumina_wcmc_bcm_bc_bi.20110521.snps.exome.sites.vcf.gz
Track type:   VCF
[h] for help:

Batch processing should exit on invaldi command

 ASCIIGenome  -b test.bed -x 'zo 3 && FOOBAR && save .png' test.bed

Should exit immediately after hitting the FOOBAR command. Instead it keeps looping.

hideTitle keeps blank line

hideTitle applied to annotation files leaves a blank one in place of the tile line instead of removing it altogether:

ASCIIGenome -g hg19 -x 'bookmark && hideTitle'
*-------------------110M----------------220M--
                                              <- This line shouldn't be here at all
||||||||||||||||||||||||||||||||||||||||||||||
58        84        110       135       161   
chr1:58-174; 117 bp; 2.5 bp/char; Mem: 1011 MB
[h] for help:

Quantitative data files are ok.

Set genome from unindexed fasta

say genome.fa does not have a .fai index attached. Command setGenome genome.fa should create the appropriate index but it doesn't:

ASCIIGenome
[h] for help: setGenome fk_hmu_pos_01.fa <-- Should create fai index and load genome

addTrack doesn't set genome

Adding a track with a dictionary should automatically set the genome if none is available. This doesn't happen:

ASCIIGenome
addTracks test_data/ds051.actb.bam
showGenome <- Sequence dictionary not available

Also setGenome:

setGenome hg19 <- OK, hg19 set
setGenome mm9 <- OK, replace with mm9
setGenome aln.hg19.bam <- Should replace mm9, but it doesn't!

Consensus sequence in BS-Seq mode

Generation of consensus sequence should be aware of BS mode so it's easier to spot variations and methylation calls. For example, you could simply use lower case c, t, y (T|C), r (A|G) for calls where ref is C and G and upper case elsewhere.

Select invalid dataCol

If dataCol command gets an invalid column (e.g. containing non-numeric data), ASCIIGenome exits with an ugly message. Fix by recovering gracefully.

GTF/GTT: Instead of displaying OOOOOO write snoRNA:snoRNA:snoRNA

This way I could more easily share the output of ASCIIgenome to others without including a legend.

Perhaps better if the separator is not :, but + for forward strand and - for reverse strand?

Reading tabix from ftp

It appears TabixReader cannot read from ftp, see samtools/htsjdk#797. This means remote tabix files on ftp cannot be read remotely.

Oops, duplicate of issue #2

Autocompletion on sequence names

It would be hugely helpful if there were a way to list all sequences in the reference genome, and use autocompletion on goto (or :) commands.

Goto non-existing location after loading sequence dictionary

The following steps lead to an uncaught exception:

Load a file without sequence dictionary. E.g.

ASCIIGenome hg19.gencode_genes_v19.gtf.gz

Go to a non existing location (allowed since there is no sequence dictionary)

goto FOOBAR

If now you load a file with dictionary like a bam file you get:

[h] for help: addTracks ear045.oxBS.actb.bam

Error processing input: [ear045.oxBS.actb.bam]

[h] for help:

That's ok-ish, error could be more informative though.

If you go to an existing location, load the bam file and move to previous position:

goto chr1 && addTracks ear045.oxBS.actb.bam && p

Exception in thread "main" java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Caused by: java.lang.NullPointerException
    at samTextViewer.GenomicCoords.getChromIdeogram(GenomicCoords.java:396)
    at samTextViewer.TrackProcessor.iterateTracks(TrackProcessor.java:41)
    at samTextViewer.Main.main(Main.java:141)
    ... 5 more

This is no good, although going to non existing locations repeatedly is something you don't normally do.

Next ignores features starting at start of chrom

If a feature starts right at the start of the chrom, next doesn't see it:

cat /tmp/tmp.bed 
Undefined_contig	0	255
Undefined_contig	1000	1155
Undefined_contig	2000	2155
Undefined_contig	3000	3155

Flip thorough the fur positions:

ASCIIGenome /tmp/tmp.bed
next
next
next
next <- Should return to interval 0-255 instead goes to 1000-1155

This works fine if 0-255 is replaced by 1-255

Adding ASCIIGenome to bioconda

I'm on it: bioconda/bioconda-recipes#2125

but will need further help/more time. Just in case sb was thinking of trying the same.

Setting genome from non-existant position

Start without any sequence dictionary:

ASCIIGenome

Now set genome, you get an error, even if the position is correctly set:

setGenome ds051.actb.bam
Error processing tracks with input [ds051.actb.bam]

This is more annoying as the track is not loaded (first you need to move to an existing location, then add the track):

ASCIIGenome
addTracks ds051.actb.bam

GTF/GFF2/GFF3 nomenclature and identification

There is a bit of confusion how ASCIIGenome recognises GTF/GFF2/GFF3 format extensions. This is how it should be:

GTF (extension .gtf) and GFF2 (ext .gff2) are the same format. So .gff2 should be processed as gtf.
GFF3 (ext .gff3) to be processed as gff.
Extension .gff should be processed as if gff3 (?? check me!)

VCF with `print`: color leaks into the printed line

The mutations in the VCF files are colored and the colour leaks into the printed lines from print

ASCIIGenome -r 1:1082518-1128598 -x 'print' CHD.exon.2010_03.sites.vcf.gz

CHD.exon.2010_03.sites.vcf.gz#1; N: 3
                  A         T       A                                                                                                                                               
1 1105468 .          G A . PASS AA=g;AC=2;AN=174;DP=1238 <- These lines are blue like the last A
1 1108138 rs61733845 C T . PASS AA=c;AC=6;AN=184;DP=1496
1 1110294 rs1320571  G A . PASS AA=A;AC=26;AN=206;DP=4605;HM2;HM3
1100950   1103524   1106099   1108673   1111247   1113822   1116396   
1:1100950-1147030; 46,081 bp; 256.0 bp/char; Mem: 129 MB

GC overhead limit exceeded

ASCIIGenome gencode.v25.annotation.gtf
Initializing coordinates... Reading file 'gencode.v25.annotation.gtf'...Exception in thread "main" java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
    at java.util.regex.Pattern.matcher(Pattern.java:1093)
    at java.lang.String.replace(String.java:2239)
    at tracks.IntervalFeature.intervalFeatureFromGtfLine(IntervalFeature.java:146)
    at tracks.IntervalFeature.<init>(IntervalFeature.java:60)
    at tracks.IntervalFeatureSet.loadFileIntoIntervalMap(IntervalFeatureSet.java:217)
    at tracks.IntervalFeatureSet.<init>(IntervalFeatureSet.java:58)
    at tracks.TrackIntervalFeature.<init>(TrackIntervalFeature.java:25)
    at samTextViewer.Main.main(Main.java:201)
    ... 5 more

Perhaps you should add something to the docs about how to increase the memory/GC size? I have no idea how to do it.

Tried on OS X and Ubuntu.

fasta files should be indexed before using, and this is not documented

I've tried running ASCIIGenome on a downloaded genome fasta file, and it returned an error as it was not indexed.

However this is not described in the documentation. Should I index it with samtools?

ASCIIGenome -fa Human.hg38.ucsc.FullSet.Nmasked.fa example.bed
Exception in thread "main" java.io.FileNotFoundException: /home/cbapps/Human.hg38.ucsc.FullSet.Nmasked.fa.fai not found.
        at htsjdk.samtools.reference.IndexedFastaSequenceFile.findRequiredFastaIndexFile(IndexedFastaSequenceFile.java:110)
        at htsjdk.samtools.reference.IndexedFastaSequen

bedGraph requires tabs, even though UCSC example is spaces

How about accepting both?

https://genome.ucsc.edu/goldenpath/help/bedgraph.html

And I did not understand what the error was because immediately after an error message is displayed, the program opens, so you never see it.

no http proxy support

It seems that download from behind a proxy doesn't work.

For example, running the following command doesn't return any output:

ASCIIGenome -g hg19 $encode/wgEncodeSydhTfbsGm10847NfkbTnfaIggrabPk.narrowPeak.gz \ $encode/wgEncodeSydhTfbsGm10847NfkbTnfaIggrabSig.bigWig \ $encode/wgEncodeSydhTfbsGm12892Pol2IggmusPk.narrowPeak.gz \ $encode/wgEncodeSydhTfbsGm12892Pol2IggmusSig.bigWig

The command seems to be stuck, and no message is shown. I assume it is trying to download the files, but no verbose output is shown. Since it is taking a lot of time, I am also guessing that it is getting no connection.

Are tabix-indexed GFFs/GTFs accepted?

GFFs takes a while to load, which is a bother since I want to visualize hundreds of regions. Therefore I am wondering whether tabix-indexed GFFs/GTFs are accepted? (Haven't been able to index any yet, seems like a hassle.)

An alternative way to solve this would be to have ASCIIGenome accept a bed file of regions to create images from, so that I would only need to load the input files once.

vcf file not showing as track.

Hi,

I'm using ASCIIGenome to visualise how reads are assigned to contigs.

NEWBLER (OLC assembler) has generated a set of contigs, I've use BWA MEM to align the the read to the contigs. I'm able to visualise this using a sorted .bam file.

Now I want to visualise the variants and proceed to use bcftools call feature to generate a .vcf file. However when i use the addTrack command, the track does not show.

If i were to individually open just the vcf file. it prints:

Cannot add file.vcf; skipping

Example BS-colouring

Hi @dariober ,

I am starting to use ASCIIGenome and would like to produce screenshots with BS-colouring. I couldn't find the notation in the documentation to do that. Can you post an example here?

Example command-line I am using:

ASCIIGenome -ni -r chr9:136946101-123456781 -x "save /data/group/test/TEST_Run001/TEST_Run001-12345678/TST59_70_1b-12345678/TST59-70-1b_S1_L001_R1_001.1.cutB_bismark_bt2_se.dedupled.sorted.bam.chr9:136946101-123456781.ascii.pdf" /data/group/test/TEST_Run001/TEST_Run001-12345678/TST59_70_1b-12345678/TST59-70-1b_S1_L001_R1_001.1.cutB_bismark_bt2_se.dedupled.sorted.bam 1>/dev/null

When using `-x <multiple gotos and saves>` only saves last region.

This is my command:

ASCIIGenome -nf -ni PolII.bed PolII_tabs.bedgraph -fa ~/genomes/hg38.fa \
 -x 'goto chr10:69223041-69223072 && save .png && goto chr3:196318127-196318155 && save .png && goto chr8:1755859-1755886 && save .png'

This is the output:

endrebak@havpryd ~/c/asciigenome> ls -latrh *png
-rw-r--r-- 1 endrebak endrebak 53K Aug  3 10:17 chr8_1755859-1755886.png

Note that

ASCIIGenome -nf -ni PolII.bed PolII_tabs.bedgraph -fa ~/genomes/hg38.fa \
 -x 'goto chr10:69223041-69223072 && save .png' \
 -x 'goto chr3:196318127-196318155 && save .png'

did not work either.

Note that if you fix this you fix #16 (creating many pngs in one go).

Sorry for the issue storm. I'll calm down now, but this seems pretty essential :)

For now I will use a loop and an indexed gtf file.

Invalid coords with range > Integer.MAX_VALUE

Need to protect against invalid range when coordinates > Integer.MAX_VALUE are requested. Reproduce:

Open a gtf file (without genome file or reference); 2) 1-4,000,000,000. This throws a java.lang.NumberFormatException but doesn't kill ASCIIGenome

But if: 1-2000000000 followed by zo you get

Exception in thread "main" java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Caused by: java.lang.RuntimeException: Invalid range: 1--1294967295
    at tracks.IntervalFeatureSet.getFeaturesInInterval(IntervalFeatureSet.java:78)
    at tracks.TrackIntervalFeature.update(TrackIntervalFeature.java:30)
    at samTextViewer.Main.main(Main.java:231)
    ... 5 more

next with feature close to position 1

Reproduce bug:

echo -e "chr1\t1000\t10000" > test.bed
ASCIIGenome -g hg19 -r chr1:1 test.bed

Then issue next command, you get:

Invalid coordinates: from: -39499;to: 50501Resetting to initial 1-2147483647
Exception in thread "main" java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Caused by: exceptions.InvalidGenomicCoordsException
    at tracks.IntervalFeatureSet.getFeaturesInInterval(IntervalFeatureSet.java:97)
    at tracks.TrackIntervalFeature.update(TrackIntervalFeature.java:38)
    at tracks.TrackIntervalFeature.<init>(TrackIntervalFeature.java:32)
    at samTextViewer.GenomicCoords.findRegex(GenomicCoords.java:701)
    at samTextViewer.Main.main(Main.java:294)
    ... 5 more

Reason:

If next is executed from position 1 (or there about) and the first feature is close to 1, after extension left and right you get a negative start position which is reset to 1-2147483647 if a genome file is present you then get this exception.

Reading tabix from ftp

It appears tabix files from ftp cannot be read. For example, read a vcf file from 1000genomes:

import htsjdk.samtools.seekablestream.SeekableStream;
import htsjdk.samtools.seekablestream.SeekableStreamFactory;
import htsjdk.tribble.readers.TabixReader;

String ftp= "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/input_call_sets/ALL.wex.union_illumina_wcmc_bcm_bc_bi.20110521.snps.exome.sites.vcf.gz";

// Here it hangs:
TabixReader tabix= new TabixReader(ftp);

// In particular, this seems to hang:
SeekableStream stream= SeekableStreamFactory
    .getInstance()
    .getBufferedStream(SeekableStreamFactory.getInstance()
    .getStreamFor(ftp));

Would be good to post on biostars/htsjdk list

Invalid bedgraoh

Instead of telling me that the chromosome does not exist it just goes to an empty region.

I tried goto 1:123-456 but the magic words were goto chr1:123-456. Instead of showing a blank region, it should tell me there is no such chromosome.

Would be neat if it understood 1 to mean chr1 and vice versa.

Invalid bedgraph opens an empy track

If an invalid bedgraph is loaded, an empty track is generated. An exception should be thrown instead.

 echo -e "chr1 0 10\nchr2 0 10" > test.bedgraph ## note space instead of tab
ASCIIGenome test.bedgraph ## Gives empty track

Corrupted TabixIndex

The tabix index created via htsjdk may skip the first interval of the first contig under certain cases. See samtools/htsjdk#393 for an example.

While we wait for htsjdk to fix this, a temporary hack may be to add a dummy first record on the files susceptible of this bug.

Rename `filter`?

Possibly todo: Rename filter to grep for consistency with Linux. Command API could be:

Include records matching. As in grep, first arg is pattern, second is file(s).

grep exon my.*bed

Include and exclude. To exclude use -v as in grep?

grep -v'mRNA exon my*.bed

Cntrl-z and then fg gives blank screen

Dunno if this is hard to fix. You only have to press enter to have the screen reappear though.

Also, pressing cntrl-z/cntrl-c/cntrl-d without meaning it is all too easy for me. Perhaps adding a prompt (Do you really want to exit) would be good?

Error stack with "Could not initilize from file"

If there are you try to load a single invalid file, you get an ugly error stack. Fix it by issuing a friendlier message. E.g.

ASCIIGenome du.tmp.txt
Initializing coordinates... 
Could not initilize from file du.tmp.txt
Reading file 'du.tmp.txt'...First line skipped. Exception in thread "main" java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Caused by: java.lang.RuntimeException: intervalFeatureFromBedLine: Invalid bed line:
[20, /nas/sblab_data1/berald01/repository/bwameth/ear020_OXBS.ecoli_fastqc/Icons]
    at tracks.IntervalFeature.intervalFeatureFromBedLine(IntervalFeature.java:115)
    at tracks.IntervalFeature.<init>(IntervalFeature.java:57)
    at tracks.IntervalFeatureSet.loadFileIntoIntervalMap(IntervalFeatureSet.java:217)
    at tracks.IntervalFeatureSet.<init>(IntervalFeatureSet.java:58)
    at tracks.TrackIntervalFeature.<init>(TrackIntervalFeature.java:25)
    at samTextViewer.Main.main(Main.java:208)
    ... 5 more

Enable changing of background color

Currently a white background is used for all text, which looks weird on terminals that have a different background color such as black (used by the super-hacker-y types). It would be great if the user could change the background color or set it to transparency.

Store command history between sessions?

Just an idea, dunno if it is hard to implement or not.

dariober / asciigenome Goto Github PK

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