[Gmod-ajax] JBrowse: Shows '=' symbol at the end of sequence in the popup

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[Gmod-ajax] JBrowse: Shows '=' symbol at the end of sequence in the popup

Dadu
Dear All,

I have installed and configured JBrowser for the visualization of alignment. I have uploaded BAM file as a track. When I click on the particular read shows the information of the sequence and its quality. I am unable to understand “=” symbol is coming along with the sequence at the end. Please someone help me in understanding what may be the reason and how to resolve that.

Thanks and regards,
Dadu




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Re: JBrowse: Shows '=' symbol at the end of sequence in the popup

Scott Cain
Hi Dadu,

Is there a public website where we can look at it?  And is this bam file available on ths site or is it something you loaded through the file menu?

Thanks,
Scott


On Mon, Feb 23, 2015 at 10:19 PM, Dadu <[hidden email]> wrote:
Dear All,

I have installed and configured JBrowser for the visualization of alignment. I have uploaded BAM file as a track. When I click on the particular read shows the information of the sequence and its quality. I am unable to understand “=” symbol is coming along with the sequence at the end. Please someone help me in understanding what may be the reason and how to resolve that.

Thanks and regards,
Dadu




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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: JBrowse: Shows '=' symbol at the end of sequence in the popup

Dadu
Hii Scott,

Please find below link to the JBrowser page. I have uploaded BAM files as tracks. Please select any one BAM file from WGRS data (named WGRS-*.bam).


Thanks and regards,
Dadu



On Thu, Feb 26, 2015 at 3:16 AM, Scott Cain <[hidden email]> wrote:
Hi Dadu,

Is there a public website where we can look at it?  And is this bam file available on ths site or is it something you loaded through the file menu?

Thanks,
Scott


On Mon, Feb 23, 2015 at 10:19 PM, Dadu <[hidden email]> wrote:
Dear All,

I have installed and configured JBrowser for the visualization of alignment. I have uploaded BAM file as a track. When I click on the particular read shows the information of the sequence and its quality. I am unable to understand “=” symbol is coming along with the sequence at the end. Please someone help me in understanding what may be the reason and how to resolve that.

Thanks and regards,
Dadu




------------------------------------------------------------------------------
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by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
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------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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Re: JBrowse: Shows '=' symbol at the end of sequence in the popup

Scott Cain
Hi Dadu,

My first guess is that there is something not quite right with the bam files themselves.  Do they show any weirdness when you use them with any other tool?

Colin, do you have any idea what's going on?

Scott


On Wed, Feb 25, 2015 at 9:48 PM, Dadu <[hidden email]> wrote:
Hii Scott,

Please find below link to the JBrowser page. I have uploaded BAM files as tracks. Please select any one BAM file from WGRS data (named WGRS-*.bam).


Thanks and regards,
Dadu




On Thu, Feb 26, 2015 at 3:16 AM, Scott Cain <[hidden email]> wrote:
Hi Dadu,

Is there a public website where we can look at it?  And is this bam file available on ths site or is it something you loaded through the file menu?

Thanks,
Scott


On Mon, Feb 23, 2015 at 10:19 PM, Dadu <[hidden email]> wrote:
Dear All,

I have installed and configured JBrowser for the visualization of alignment. I have uploaded BAM file as a track. When I click on the particular read shows the information of the sequence and its quality. I am unable to understand “=” symbol is coming along with the sequence at the end. Please someone help me in understanding what may be the reason and how to resolve that.

Thanks and regards,
Dadu




------------------------------------------------------------------------------
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by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
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------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: JBrowse: Shows '=' symbol at the end of sequence in the popup

Keiran Raine
Hi,

Quickly doing "save track", view as gff3 shows the read seq ending %3d (=). I was hoping to view as SAM to completely diagnose so can you do "samtools view" and paste a few records into an email?

Cheers,

Keiran

Sent from my Android phone using TouchDown (www.nitrodesk.com)

-----Original Message-----
From: Scott Cain [[hidden email]]
Received: Thursday, 26 Feb 2015, 17:01
To: Dadu [[hidden email]]; Colin D [[hidden email]]
CC: [hidden email] [[hidden email]]
Subject: Re: [Gmod-ajax] JBrowse: Shows '=' symbol at the end of sequence in the popup

Hi Dadu,

My first guess is that there is something not quite right with the bam files themselves.  Do they show any weirdness when you use them with any other tool?

Colin, do you have any idea what's going on?

Scott


On Wed, Feb 25, 2015 at 9:48 PM, Dadu <[hidden email]> wrote:
Hii Scott,

Please find below link to the JBrowser page. I have uploaded BAM files as tracks. Please select any one BAM file from WGRS data (named WGRS-*.bam).


Thanks and regards,
Dadu




On Thu, Feb 26, 2015 at 3:16 AM, Scott Cain <[hidden email]> wrote:
Hi Dadu,

Is there a public website where we can look at it?  And is this bam file available on ths site or is it something you loaded through the file menu?

Thanks,
Scott


On Mon, Feb 23, 2015 at 10:19 PM, Dadu <[hidden email]> wrote:
Dear All,

I have installed and configured JBrowser for the visualization of alignment. I have uploaded BAM file as a track. When I click on the particular read shows the information of the sequence and its quality. I am unable to understand “=” symbol is coming along with the sequence at the end. Please someone help me in understanding what may be the reason and how to resolve that.

Thanks and regards,
Dadu




------------------------------------------------------------------------------
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by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="&#43;12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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Re: JBrowse: Shows '=' symbol at the end of sequence in the popup

Thomas Down
In reply to this post by Scott Cain
I think the problem lies here:


Because sequences in BAM files are nybble-packed (two bases to a byte), reads with an odd number of bases have a wasted nybble at the end of the sequence, which is getting decoded to the '=' character.

This isn't a big deal if you're rendering an alignment to the genome (taking into account the CIGAR line), but is an annoyance if you just want to see the raw sequence of the read.  Since the length of the read is recorded, it's just a matter of trimming off the last base of the read when necessary.

            Thomas.

On Thu, Feb 26, 2015 at 4:58 PM, Scott Cain <[hidden email]> wrote:
Hi Dadu,

My first guess is that there is something not quite right with the bam files themselves.  Do they show any weirdness when you use them with any other tool?

Colin, do you have any idea what's going on?

Scott


On Wed, Feb 25, 2015 at 9:48 PM, Dadu <[hidden email]> wrote:
Hii Scott,

Please find below link to the JBrowser page. I have uploaded BAM files as tracks. Please select any one BAM file from WGRS data (named WGRS-*.bam).


Thanks and regards,
Dadu




On Thu, Feb 26, 2015 at 3:16 AM, Scott Cain <[hidden email]> wrote:
Hi Dadu,

Is there a public website where we can look at it?  And is this bam file available on ths site or is it something you loaded through the file menu?

Thanks,
Scott


On Mon, Feb 23, 2015 at 10:19 PM, Dadu <[hidden email]> wrote:
Dear All,

I have installed and configured JBrowser for the visualization of alignment. I have uploaded BAM file as a track. When I click on the particular read shows the information of the sequence and its quality. I am unable to understand “=” symbol is coming along with the sequence at the end. Please someone help me in understanding what may be the reason and how to resolve that.

Thanks and regards,
Dadu




------------------------------------------------------------------------------
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by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

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Re: JBrowse: Shows '=' symbol at the end of sequence in the popup

Dadu
Dear Thomas,

Thank you for your response. I think you are right. BAM file which are of RAD sequencing type contains the read length of 100 base pair won't show ‘=’ symbol at the end but the WGRS sequencing read length is 101 base pair. I would like to retain the complete read sequence (101 base pair). Is there any way to change in the LazyFeature.js to avoid ‘=’ symbol and retain 101 base pair?

Thanks and regards,
Dadu



On Fri, Feb 27, 2015 at 1:26 AM, Thomas Down <[hidden email]> wrote:
I think the problem lies here:


Because sequences in BAM files are nybble-packed (two bases to a byte), reads with an odd number of bases have a wasted nybble at the end of the sequence, which is getting decoded to the '=' character.

This isn't a big deal if you're rendering an alignment to the genome (taking into account the CIGAR line), but is an annoyance if you just want to see the raw sequence of the read.  Since the length of the read is recorded, it's just a matter of trimming off the last base of the read when necessary.

            Thomas.

On Thu, Feb 26, 2015 at 4:58 PM, Scott Cain <[hidden email]> wrote:
Hi Dadu,

My first guess is that there is something not quite right with the bam files themselves.  Do they show any weirdness when you use them with any other tool?

Colin, do you have any idea what's going on?

Scott


On Wed, Feb 25, 2015 at 9:48 PM, Dadu <[hidden email]> wrote:
Hii Scott,

Please find below link to the JBrowser page. I have uploaded BAM files as tracks. Please select any one BAM file from WGRS data (named WGRS-*.bam).


Thanks and regards,
Dadu




On Thu, Feb 26, 2015 at 3:16 AM, Scott Cain <[hidden email]> wrote:
Hi Dadu,

Is there a public website where we can look at it?  And is this bam file available on ths site or is it something you loaded through the file menu?

Thanks,
Scott


On Mon, Feb 23, 2015 at 10:19 PM, Dadu <[hidden email]> wrote:
Dear All,

I have installed and configured JBrowser for the visualization of alignment. I have uploaded BAM file as a track. When I click on the particular read shows the information of the sequence and its quality. I am unable to understand “=” symbol is coming along with the sequence at the end. Please someone help me in understanding what may be the reason and how to resolve that.

Thanks and regards,
Dadu




------------------------------------------------------------------------------
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by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
_______________________________________________
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

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Re: JBrowse: Shows '=' symbol at the end of sequence in the popup

Thomas Down
Untested but I think this will work:

    seq: function() {
        var seq = '';
        var byteArray = this.bytes.byteArray;
        var p = this.bytes.start + 36 + this._get('_l_read_name') + this._get('_n_cigar_op')*4;
        var seqLength = this._get('seq_length');
        var seqBytes = (seqLength + 1) >> 1;
        for (var j = 0; j < seqBytes; ++j) {
            var sb = byteArray[p + j];
            seq += SEQRET_DECODER[(sb & 0xf0) >> 4];
            if (seq.length < seqLength)
                seq += SEQRET_DECODER[(sb & 0x0f)];
        }
        return seq;
    },

Thomas.

On Fri, Feb 27, 2015 at 4:53 AM, Dadu <[hidden email]> wrote:
Dear Thomas,

Thank you for your response. I think you are right. BAM file which are of RAD sequencing type contains the read length of 100 base pair won't show ‘=’ symbol at the end but the WGRS sequencing read length is 101 base pair. I would like to retain the complete read sequence (101 base pair). Is there any way to change in the LazyFeature.js to avoid ‘=’ symbol and retain 101 base pair?

Thanks and regards,
Dadu



On Fri, Feb 27, 2015 at 1:26 AM, Thomas Down <[hidden email]> wrote:
I think the problem lies here:


Because sequences in BAM files are nybble-packed (two bases to a byte), reads with an odd number of bases have a wasted nybble at the end of the sequence, which is getting decoded to the '=' character.

This isn't a big deal if you're rendering an alignment to the genome (taking into account the CIGAR line), but is an annoyance if you just want to see the raw sequence of the read.  Since the length of the read is recorded, it's just a matter of trimming off the last base of the read when necessary.

            Thomas.

On Thu, Feb 26, 2015 at 4:58 PM, Scott Cain <[hidden email]> wrote:
Hi Dadu,

My first guess is that there is something not quite right with the bam files themselves.  Do they show any weirdness when you use them with any other tool?

Colin, do you have any idea what's going on?

Scott


On Wed, Feb 25, 2015 at 9:48 PM, Dadu <[hidden email]> wrote:
Hii Scott,

Please find below link to the JBrowser page. I have uploaded BAM files as tracks. Please select any one BAM file from WGRS data (named WGRS-*.bam).


Thanks and regards,
Dadu




On Thu, Feb 26, 2015 at 3:16 AM, Scott Cain <[hidden email]> wrote:
Hi Dadu,

Is there a public website where we can look at it?  And is this bam file available on ths site or is it something you loaded through the file menu?

Thanks,
Scott


On Mon, Feb 23, 2015 at 10:19 PM, Dadu <[hidden email]> wrote:
Dear All,

I have installed and configured JBrowser for the visualization of alignment. I have uploaded BAM file as a track. When I click on the particular read shows the information of the sequence and its quality. I am unable to understand “=” symbol is coming along with the sequence at the end. Please someone help me in understanding what may be the reason and how to resolve that.

Thanks and regards,
Dadu




------------------------------------------------------------------------------
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by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
_______________________________________________
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

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Re: JBrowse: Shows '=' symbol at the end of sequence in the popup

Dadu
Dear All,

These lines fixed the issue which I was facing. Thanks to all.

Thanks and regards,
Dadu


On Fri, Feb 27, 2015 at 12:36 PM, Thomas Down <[hidden email]> wrote:
Untested but I think this will work:

    seq: function() {
        var seq = '';
        var byteArray = this.bytes.byteArray;
        var p = this.bytes.start + 36 + this._get('_l_read_name') + this._get('_n_cigar_op')*4;
        var seqLength = this._get('seq_length');
        var seqBytes = (seqLength + 1) >> 1;
        for (var j = 0; j < seqBytes; ++j) {
            var sb = byteArray[p + j];
            seq += SEQRET_DECODER[(sb & 0xf0) >> 4];
            if (seq.length < seqLength)
                seq += SEQRET_DECODER[(sb & 0x0f)];
        }
        return seq;
    },

Thomas.

On Fri, Feb 27, 2015 at 4:53 AM, Dadu <[hidden email]> wrote:
Dear Thomas,

Thank you for your response. I think you are right. BAM file which are of RAD sequencing type contains the read length of 100 base pair won't show ‘=’ symbol at the end but the WGRS sequencing read length is 101 base pair. I would like to retain the complete read sequence (101 base pair). Is there any way to change in the LazyFeature.js to avoid ‘=’ symbol and retain 101 base pair?

Thanks and regards,
Dadu



On Fri, Feb 27, 2015 at 1:26 AM, Thomas Down <[hidden email]> wrote:
I think the problem lies here:


Because sequences in BAM files are nybble-packed (two bases to a byte), reads with an odd number of bases have a wasted nybble at the end of the sequence, which is getting decoded to the '=' character.

This isn't a big deal if you're rendering an alignment to the genome (taking into account the CIGAR line), but is an annoyance if you just want to see the raw sequence of the read.  Since the length of the read is recorded, it's just a matter of trimming off the last base of the read when necessary.

            Thomas.

On Thu, Feb 26, 2015 at 4:58 PM, Scott Cain <[hidden email]> wrote:
Hi Dadu,

My first guess is that there is something not quite right with the bam files themselves.  Do they show any weirdness when you use them with any other tool?

Colin, do you have any idea what's going on?

Scott


On Wed, Feb 25, 2015 at 9:48 PM, Dadu <[hidden email]> wrote:
Hii Scott,

Please find below link to the JBrowser page. I have uploaded BAM files as tracks. Please select any one BAM file from WGRS data (named WGRS-*.bam).


Thanks and regards,
Dadu




On Thu, Feb 26, 2015 at 3:16 AM, Scott Cain <[hidden email]> wrote:
Hi Dadu,

Is there a public website where we can look at it?  And is this bam file available on ths site or is it something you loaded through the file menu?

Thanks,
Scott


On Mon, Feb 23, 2015 at 10:19 PM, Dadu <[hidden email]> wrote:
Dear All,

I have installed and configured JBrowser for the visualization of alignment. I have uploaded BAM file as a track. When I click on the particular read shows the information of the sequence and its quality. I am unable to understand “=” symbol is coming along with the sequence at the end. Please someone help me in understanding what may be the reason and how to resolve that.

Thanks and regards,
Dadu




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------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

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Re: JBrowse: Shows '=' symbol at the end of sequence in the popup

Suzanna Lewis-3
In reply to this post by Thomas Down
Chris or Nathan,

Would you please make sure this fix gets into the main trunk please.

-S

On Thu, Feb 26, 2015 at 11:06 PM, Thomas Down <[hidden email]> wrote:
Untested but I think this will work:

    seq: function() {
        var seq = '';
        var byteArray = this.bytes.byteArray;
        var p = this.bytes.start + 36 + this._get('_l_read_name') + this._get('_n_cigar_op')*4;
        var seqLength = this._get('seq_length');
        var seqBytes = (seqLength + 1) >> 1;
        for (var j = 0; j < seqBytes; ++j) {
            var sb = byteArray[p + j];
            seq += SEQRET_DECODER[(sb & 0xf0) >> 4];
            if (seq.length < seqLength)
                seq += SEQRET_DECODER[(sb & 0x0f)];
        }
        return seq;
    },

Thomas.

On Fri, Feb 27, 2015 at 4:53 AM, Dadu <[hidden email]> wrote:
Dear Thomas,

Thank you for your response. I think you are right. BAM file which are of RAD sequencing type contains the read length of 100 base pair won't show ‘=’ symbol at the end but the WGRS sequencing read length is 101 base pair. I would like to retain the complete read sequence (101 base pair). Is there any way to change in the LazyFeature.js to avoid ‘=’ symbol and retain 101 base pair?

Thanks and regards,
Dadu



On Fri, Feb 27, 2015 at 1:26 AM, Thomas Down <[hidden email]> wrote:
I think the problem lies here:


Because sequences in BAM files are nybble-packed (two bases to a byte), reads with an odd number of bases have a wasted nybble at the end of the sequence, which is getting decoded to the '=' character.

This isn't a big deal if you're rendering an alignment to the genome (taking into account the CIGAR line), but is an annoyance if you just want to see the raw sequence of the read.  Since the length of the read is recorded, it's just a matter of trimming off the last base of the read when necessary.

            Thomas.

On Thu, Feb 26, 2015 at 4:58 PM, Scott Cain <[hidden email]> wrote:
Hi Dadu,

My first guess is that there is something not quite right with the bam files themselves.  Do they show any weirdness when you use them with any other tool?

Colin, do you have any idea what's going on?

Scott


On Wed, Feb 25, 2015 at 9:48 PM, Dadu <[hidden email]> wrote:
Hii Scott,

Please find below link to the JBrowser page. I have uploaded BAM files as tracks. Please select any one BAM file from WGRS data (named WGRS-*.bam).


Thanks and regards,
Dadu




On Thu, Feb 26, 2015 at 3:16 AM, Scott Cain <[hidden email]> wrote:
Hi Dadu,

Is there a public website where we can look at it?  And is this bam file available on ths site or is it something you loaded through the file menu?

Thanks,
Scott


On Mon, Feb 23, 2015 at 10:19 PM, Dadu <[hidden email]> wrote:
Dear All,

I have installed and configured JBrowser for the visualization of alignment. I have uploaded BAM file as a track. When I click on the particular read shows the information of the sequence and its quality. I am unable to understand “=” symbol is coming along with the sequence at the end. Please someone help me in understanding what may be the reason and how to resolve that.

Thanks and regards,
Dadu




------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

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news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
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things parallel software development, from weekly thought leadership blogs to
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Re: JBrowse: Shows '=' symbol at the end of sequence in the popup

Colin
Thanks for catching and fixing that, patch looks fine! It's on the jbrowse github now.


-Colin

On Sun, Mar 1, 2015 at 8:45 PM, Suzanna Lewis <[hidden email]> wrote:
Chris or Nathan,

Would you please make sure this fix gets into the main trunk please.

-S

On Thu, Feb 26, 2015 at 11:06 PM, Thomas Down <[hidden email]> wrote:
Untested but I think this will work:

    seq: function() {
        var seq = '';
        var byteArray = this.bytes.byteArray;
        var p = this.bytes.start + 36 + this._get('_l_read_name') + this._get('_n_cigar_op')*4;
        var seqLength = this._get('seq_length');
        var seqBytes = (seqLength + 1) >> 1;
        for (var j = 0; j < seqBytes; ++j) {
            var sb = byteArray[p + j];
            seq += SEQRET_DECODER[(sb & 0xf0) >> 4];
            if (seq.length < seqLength)
                seq += SEQRET_DECODER[(sb & 0x0f)];
        }
        return seq;
    },

Thomas.

On Fri, Feb 27, 2015 at 4:53 AM, Dadu <[hidden email]> wrote:
Dear Thomas,

Thank you for your response. I think you are right. BAM file which are of RAD sequencing type contains the read length of 100 base pair won't show ‘=’ symbol at the end but the WGRS sequencing read length is 101 base pair. I would like to retain the complete read sequence (101 base pair). Is there any way to change in the LazyFeature.js to avoid ‘=’ symbol and retain 101 base pair?

Thanks and regards,
Dadu



On Fri, Feb 27, 2015 at 1:26 AM, Thomas Down <[hidden email]> wrote:
I think the problem lies here:


Because sequences in BAM files are nybble-packed (two bases to a byte), reads with an odd number of bases have a wasted nybble at the end of the sequence, which is getting decoded to the '=' character.

This isn't a big deal if you're rendering an alignment to the genome (taking into account the CIGAR line), but is an annoyance if you just want to see the raw sequence of the read.  Since the length of the read is recorded, it's just a matter of trimming off the last base of the read when necessary.

            Thomas.

On Thu, Feb 26, 2015 at 4:58 PM, Scott Cain <[hidden email]> wrote:
Hi Dadu,

My first guess is that there is something not quite right with the bam files themselves.  Do they show any weirdness when you use them with any other tool?

Colin, do you have any idea what's going on?

Scott


On Wed, Feb 25, 2015 at 9:48 PM, Dadu <[hidden email]> wrote:
Hii Scott,

Please find below link to the JBrowser page. I have uploaded BAM files as tracks. Please select any one BAM file from WGRS data (named WGRS-*.bam).


Thanks and regards,
Dadu




On Thu, Feb 26, 2015 at 3:16 AM, Scott Cain <[hidden email]> wrote:
Hi Dadu,

Is there a public website where we can look at it?  And is this bam file available on ths site or is it something you loaded through the file menu?

Thanks,
Scott


On Mon, Feb 23, 2015 at 10:19 PM, Dadu <[hidden email]> wrote:
Dear All,

I have installed and configured JBrowser for the visualization of alignment. I have uploaded BAM file as a track. When I click on the particular read shows the information of the sequence and its quality. I am unable to understand “=” symbol is coming along with the sequence at the end. Please someone help me in understanding what may be the reason and how to resolve that.

Thanks and regards,
Dadu




------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax





------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
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by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
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things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
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