[Gmod-ajax] Error converting BAM to JSON for browsing in Jbrowse

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[Gmod-ajax] Error converting BAM to JSON for browsing in Jbrowse

sanjay shah
Hi,

I have a BAM file   and when i execute the following command  to
convert the BAM to Json :

$$ bin/flatfile-to-json.pl  --bam
/var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon
--tracklabel BAM_data --key "BAM Data"

I get the following error;

No index file for
/var/www/jbrowse/docs/tutorial/data_files/20100311.bam; try opening
file with -autoindex at /usr/local/lib/perl/5.10.0/Bio/DB/Sam.pm line
1940

I have installed the  prerequisite installed for browsing BAM files in
Jbrowse .I also have  the corresponding reference file in Json  and am
able to browse in Jbrowse.


Do we have to create any index for browsing BAM files in Jbrowse
before we convert it to Json .Please help  me in resolving the
following error.



Thanks,
Sanjay

--
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Re: Error converting BAM to JSON for browsing in Jbrowse

Mitch Skinner
In the future, JBrowse will probably use the autoindexing option as
suggested by that error message.

Right now, though, you can get around this by creating the index
manually with samtools; you'd write something like:

$ samtools index /var/www/jbrowse/docs/tutorial/data_files/20100311.bam

(using the full path to the samtools program if it's not in your path)

Mitch

On 06/22/2010 02:12 AM, sanjay shah wrote:

> Hi,
>
> I have a BAM file   and when i execute the following command  to
> convert the BAM to Json :
>
> $$ bin/flatfile-to-json.pl  --bam
> /var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon
> --tracklabel BAM_data --key "BAM Data"
>
> I get the following error;
>
> No index file for
> /var/www/jbrowse/docs/tutorial/data_files/20100311.bam; try opening
> file with -autoindex at /usr/local/lib/perl/5.10.0/Bio/DB/Sam.pm line
> 1940
>
> I have installed the  prerequisite installed for browsing BAM files in
> Jbrowse .I also have  the corresponding reference file in Json  and am
> able to browse in Jbrowse.
>
>
> Do we have to create any index for browsing BAM files in Jbrowse
> before we convert it to Json .Please help  me in resolving the
> following error.
>
>
>
> Thanks,
> Sanjay
>
>    


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Re: Error converting BAM to JSON for browsing in Jbrowse

sanjay shah
Hi ,

Thanks.I  did sort  the alignments and  then  created index manually
with samtools( I  have "20100311.sorted.bam.bai " file ) ; now when I
again try to convert BAM to JSON by issuing command as:


 $$ bin/flatfile-to-json.pl  --bam
 /var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon
 --tracklabel BAM_data --key "BAM Data"


I get  following error:

Use of uninitialized value in int at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25.
Use of uninitialized value in int at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25.
Use of uninitialized value in int at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25.
Use of uninitialized value in int at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25.



Please help on this aspect ..Thanks


Thanks,
Sanjay


On Tue, Jun 22, 2010 at 6:52 PM, Mitch Skinner
<[hidden email]> wrote:

> In the future, JBrowse will probably use the autoindexing option as
> suggested by that error message.
>
> Right now, though, you can get around this by creating the index manually
> with samtools; you'd write something like:
>
> $ samtools index /var/www/jbrowse/docs/tutorial/data_files/20100311.bam
>
> (using the full path to the samtools program if it's not in your path)
>
> Mitch
>
> On 06/22/2010 02:12 AM, sanjay shah wrote:
>>
>> Hi,
>>
>> I have a BAM file   and when i execute the following command  to
>> convert the BAM to Json :
>>
>> $$ bin/flatfile-to-json.pl  --bam
>> /var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon
>> --tracklabel BAM_data --key "BAM Data"
>>
>> I get the following error;
>>
>> No index file for
>> /var/www/jbrowse/docs/tutorial/data_files/20100311.bam; try opening
>> file with -autoindex at /usr/local/lib/perl/5.10.0/Bio/DB/Sam.pm line
>> 1940
>>
>> I have installed the  prerequisite installed for browsing BAM files in
>> Jbrowse .I also have  the corresponding reference file in Json  and am
>> able to browse in Jbrowse.
>>
>>
>> Do we have to create any index for browsing BAM files in Jbrowse
>> before we convert it to Json .Please help  me in resolving the
>> following error.
>>
>>
>>
>> Thanks,
>> Sanjay
>>
>>
>
>



--
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Re: Error converting BAM to JSON for browsing in Jbrowse

sanjay shah
Hi ,


Sorry Typo error in the earlier mail ..

   The bam file is "20100311.sorted.bam"  and not "20100311.bam"
that is being provided in the command after index has been created  as
:
  " 20100311.sorted.bam.bai ."..
So the command  executed is :
 $$ bin/flatfile-to-json.pl  --bam
  /var/www/jbrowse/docs/tutorial/data_files20100311.sorted.bam --cssclass exon
  --tracklabel BAM_data --key "BAM Data"


 which   throws the  following error

Use of uninitialized value in int at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25.
Use of uninitialized value in int at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25.
Use of uninitialized value in int at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25.
Use of uninitialized value in int at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25.
Use of uninitialized value in int at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.


please help ..Thanks

Thanks,
Sanjay




Thanks,
Sanjay

On Wed, Jun 23, 2010 at 2:10 PM, sanjay shah <[hidden email]> wrote:

> Hi ,
>
> Thanks.I  did sort  the alignments and  then  created index manually
> with samtools( I  have "20100311.sorted.bam.bai " file ) ; now when I
> again try to convert BAM to JSON by issuing command as:
>
>
>  $$ bin/flatfile-to-json.pl  --bam
>  /var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon
>  --tracklabel BAM_data --key "BAM Data"
>
>
> I get  following error:
>
> Use of uninitialized value in int at
> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27.
> Use of uninitialized value in subtraction (-) at
> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25.
> Use of uninitialized value in int at
> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27.
> Use of uninitialized value in subtraction (-) at
> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25.
> Use of uninitialized value in int at
> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27.
> Use of uninitialized value in subtraction (-) at
> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25.
> Use of uninitialized value in int at
> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27.
> Use of uninitialized value in subtraction (-) at
> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25.
>
>
>
> Please help on this aspect ..Thanks
>
>
> Thanks,
> Sanjay
>
>
> On Tue, Jun 22, 2010 at 6:52 PM, Mitch Skinner
> <[hidden email]> wrote:
>> In the future, JBrowse will probably use the autoindexing option as
>> suggested by that error message.
>>
>> Right now, though, you can get around this by creating the index manually
>> with samtools; you'd write something like:
>>
>> $ samtools index /var/www/jbrowse/docs/tutorial/data_files/20100311.bam
>>
>> (using the full path to the samtools program if it's not in your path)
>>
>> Mitch
>>
>> On 06/22/2010 02:12 AM, sanjay shah wrote:
>>>
>>> Hi,
>>>
>>> I have a BAM file   and when i execute the following command  to
>>> convert the BAM to Json :
>>>
>>> $$ bin/flatfile-to-json.pl  --bam
>>> /var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon
>>> --tracklabel BAM_data --key "BAM Data"
>>>
>>> I get the following error;
>>>
>>> No index file for
>>> /var/www/jbrowse/docs/tutorial/data_files/20100311.bam; try opening
>>> file with -autoindex at /usr/local/lib/perl/5.10.0/Bio/DB/Sam.pm line
>>> 1940
>>>
>>> I have installed the  prerequisite installed for browsing BAM files in
>>> Jbrowse .I also have  the corresponding reference file in Json  and am
>>> able to browse in Jbrowse.
>>>
>>>
>>> Do we have to create any index for browsing BAM files in Jbrowse
>>> before we convert it to Json .Please help  me in resolving the
>>> following error.
>>>
>>>
>>>
>>> Thanks,
>>> Sanjay
>>>
>>>
>>
>>
>
>
>
> --
> Success is how many times u smile each day every day.
>



--
Success is how many times u smile each day every day.

------------------------------------------------------------------------------
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GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
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Re: Error converting BAM to JSON for browsing in Jbrowse

Mitch Skinner
Hi,

I've seen this but I haven't yet figured out exactly what's going on.  I
think it has something to do with paired-end reads, and it might be
caused by reads whose pair-mate isn't mapped.

Handling paired-end reads better is something I'm currently working on.

Mitch

On 06/23/2010 01:35 AM, sanjay shah wrote:

> Hi ,
>
>
> Sorry Typo error in the earlier mail ..
>
>     The bam file is "20100311.sorted.bam"  and not "20100311.bam"
> that is being provided in the command after index has been created  as
> :
>    " 20100311.sorted.bam.bai ."..
> So the command  executed is :
>   $$ bin/flatfile-to-json.pl  --bam
>    /var/www/jbrowse/docs/tutorial/data_files20100311.sorted.bam --cssclass exon
>    --tracklabel BAM_data --key "BAM Data"
>
>
>   which   throws the  following error
>
> Use of uninitialized value in int at
> /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
> Use of uninitialized value in subtraction (-) at
> /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25.
> Use of uninitialized value in int at
> /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
> Use of uninitialized value in subtraction (-) at
> /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25.
> Use of uninitialized value in int at
> /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
> Use of uninitialized value in subtraction (-) at
> /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25.
> Use of uninitialized value in int at
> /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
> Use of uninitialized value in subtraction (-) at
> /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25.
> Use of uninitialized value in int at
> /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
>
>
> please help ..Thanks
>
> Thanks,
> Sanjay
>
>
>
>
> Thanks,
> Sanjay
>
> On Wed, Jun 23, 2010 at 2:10 PM, sanjay shah<[hidden email]>  wrote:
>    
>> Hi ,
>>
>> Thanks.I  did sort  the alignments and  then  created index manually
>> with samtools( I  have "20100311.sorted.bam.bai " file ) ; now when I
>> again try to convert BAM to JSON by issuing command as:
>>
>>
>>   $$ bin/flatfile-to-json.pl  --bam
>>   /var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon
>>   --tracklabel BAM_data --key "BAM Data"
>>
>>
>> I get  following error:
>>
>> Use of uninitialized value in int at
>> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27.
>> Use of uninitialized value in subtraction (-) at
>> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25.
>> Use of uninitialized value in int at
>> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27.
>> Use of uninitialized value in subtraction (-) at
>> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25.
>> Use of uninitialized value in int at
>> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27.
>> Use of uninitialized value in subtraction (-) at
>> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25.
>> Use of uninitialized value in int at
>> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27.
>> Use of uninitialized value in subtraction (-) at
>> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25.
>>
>>
>>
>> Please help on this aspect ..Thanks
>>
>>
>> Thanks,
>> Sanjay
>>
>>
>> On Tue, Jun 22, 2010 at 6:52 PM, Mitch Skinner
>> <[hidden email]>  wrote:
>>      
>>> In the future, JBrowse will probably use the autoindexing option as
>>> suggested by that error message.
>>>
>>> Right now, though, you can get around this by creating the index manually
>>> with samtools; you'd write something like:
>>>
>>> $ samtools index /var/www/jbrowse/docs/tutorial/data_files/20100311.bam
>>>
>>> (using the full path to the samtools program if it's not in your path)
>>>
>>> Mitch
>>>
>>> On 06/22/2010 02:12 AM, sanjay shah wrote:
>>>        
>>>> Hi,
>>>>
>>>> I have a BAM file   and when i execute the following command  to
>>>> convert the BAM to Json :
>>>>
>>>> $$ bin/flatfile-to-json.pl  --bam
>>>> /var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon
>>>> --tracklabel BAM_data --key "BAM Data"
>>>>
>>>> I get the following error;
>>>>
>>>> No index file for
>>>> /var/www/jbrowse/docs/tutorial/data_files/20100311.bam; try opening
>>>> file with -autoindex at /usr/local/lib/perl/5.10.0/Bio/DB/Sam.pm line
>>>> 1940
>>>>
>>>> I have installed the  prerequisite installed for browsing BAM files in
>>>> Jbrowse .I also have  the corresponding reference file in Json  and am
>>>> able to browse in Jbrowse.
>>>>
>>>>
>>>> Do we have to create any index for browsing BAM files in Jbrowse
>>>> before we convert it to Json .Please help  me in resolving the
>>>> following error.
>>>>
>>>>
>>>>
>>>> Thanks,
>>>> Sanjay
>>>>
>>>>
>>>>          
>>>
>>>        
>>
>>
>> --
>> Success is how many times u smile each day every day.
>>
>>      
>
>
>    


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Re: Error converting BAM to JSON for browsing in Jbrowse

sanjay shah
Hi Mitch,

Thanks .But do that error really hampers the functionality of BAM files being visualized in Jbrowse(I mean is there any data ,information loss  due to this  in BAM to JSON conversion and visualization in Jbrowse.



Thanks,
Sanjay

On Thu, Jul 1, 2010 at 8:12 PM, Mitch Skinner <[hidden email]> wrote:
Hi,

I've seen this but I haven't yet figured out exactly what's going on.  I think it has something to do with paired-end reads, and it might be caused by reads whose pair-mate isn't mapped.

Handling paired-end reads better is something I'm currently working on.

Mitch


On 06/23/2010 01:35 AM, sanjay shah wrote:
Hi ,


Sorry Typo error in the earlier mail ..

   The bam file is "20100311.sorted.bam"  and not "20100311.bam"
that is being provided in the command after index has been created  as
:
  " 20100311.sorted.bam.bai ."..
So the command  executed is :
 $$ bin/flatfile-to-json.pl  --bam
  /var/www/jbrowse/docs/tutorial/data_files20100311.sorted.bam --cssclass exon
  --tracklabel BAM_data --key "BAM Data"


 which   throws the  following error

Use of uninitialized value in int at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25.
Use of uninitialized value in int at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25.
Use of uninitialized value in int at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25.
Use of uninitialized value in int at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25.
Use of uninitialized value in int at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.


please help ..Thanks

Thanks,
Sanjay




Thanks,
Sanjay

On Wed, Jun 23, 2010 at 2:10 PM, sanjay shah<[hidden email]>  wrote:
 
Hi ,

Thanks.I  did sort  the alignments and  then  created index manually
with samtools( I  have "20100311.sorted.bam.bai " file ) ; now when I
again try to convert BAM to JSON by issuing command as:


 $$ bin/flatfile-to-json.pl  --bam
 /var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon
 --tracklabel BAM_data --key "BAM Data"


I get  following error:

Use of uninitialized value in int at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25.
Use of uninitialized value in int at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25.
Use of uninitialized value in int at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25.
Use of uninitialized value in int at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25.



Please help on this aspect ..Thanks


Thanks,
Sanjay


On Tue, Jun 22, 2010 at 6:52 PM, Mitch Skinner
<[hidden email]>  wrote:
   
In the future, JBrowse will probably use the autoindexing option as
suggested by that error message.

Right now, though, you can get around this by creating the index manually
with samtools; you'd write something like:

$ samtools index /var/www/jbrowse/docs/tutorial/data_files/20100311.bam

(using the full path to the samtools program if it's not in your path)

Mitch

On 06/22/2010 02:12 AM, sanjay shah wrote:
     
Hi,

I have a BAM file   and when i execute the following command  to
convert the BAM to Json :

$$ bin/flatfile-to-json.pl  --bam
/var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon
--tracklabel BAM_data --key "BAM Data"

I get the following error;

No index file for
/var/www/jbrowse/docs/tutorial/data_files/20100311.bam; try opening
file with -autoindex at /usr/local/lib/perl/5.10.0/Bio/DB/Sam.pm line
1940

I have installed the  prerequisite installed for browsing BAM files in
Jbrowse .I also have  the corresponding reference file in Json  and am
able to browse in Jbrowse.


Do we have to create any index for browsing BAM files in Jbrowse
before we convert it to Json .Please help  me in resolving the
following error.



Thanks,
Sanjay


       

     


--
Success is how many times u smile each day every day.

   


 




--
Success is how many times u smile each day every day.

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Re: Error converting BAM to JSON for browsing in Jbrowse

Mitch Skinner
Yes.  It's a bug, I'm aware of it, and I'm working on it, just like all the other bugs and shortcomings in JBrowse.  You've encountered the frontier of active JBrowse development, on the development branch.

Mitch

On 07/02/2010 12:01 AM, sanjay shah wrote:
Hi Mitch,

Thanks .But do that error really hampers the functionality of BAM files being visualized in Jbrowse(I mean is there any data ,information loss  due to this  in BAM to JSON conversion and visualization in Jbrowse.



Thanks,
Sanjay

On Thu, Jul 1, 2010 at 8:12 PM, Mitch Skinner <[hidden email]> wrote:
Hi,

I've seen this but I haven't yet figured out exactly what's going on.  I think it has something to do with paired-end reads, and it might be caused by reads whose pair-mate isn't mapped.

Handling paired-end reads better is something I'm currently working on.

Mitch


On 06/23/2010 01:35 AM, sanjay shah wrote:
Hi ,


Sorry Typo error in the earlier mail ..

   The bam file is "20100311.sorted.bam"  and not "20100311.bam"
that is being provided in the command after index has been created  as
:
  " 20100311.sorted.bam.bai ."..
So the command  executed is :
 $$ bin/flatfile-to-json.pl  --bam
  /var/www/jbrowse/docs/tutorial/data_files20100311.sorted.bam --cssclass exon
  --tracklabel BAM_data --key "BAM Data"


 which   throws the  following error

Use of uninitialized value in int at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25.
Use of uninitialized value in int at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25.
Use of uninitialized value in int at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25.
Use of uninitialized value in int at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25.
Use of uninitialized value in int at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.


please help ..Thanks

Thanks,
Sanjay




Thanks,
Sanjay

On Wed, Jun 23, 2010 at 2:10 PM, sanjay shah<[hidden email]>  wrote:
 
Hi ,

Thanks.I  did sort  the alignments and  then  created index manually
with samtools( I  have "20100311.sorted.bam.bai " file ) ; now when I
again try to convert BAM to JSON by issuing command as:


 $$ bin/flatfile-to-json.pl  --bam
 /var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon
 --tracklabel BAM_data --key "BAM Data"


I get  following error:

Use of uninitialized value in int at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25.
Use of uninitialized value in int at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25.
Use of uninitialized value in int at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25.
Use of uninitialized value in int at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25.



Please help on this aspect ..Thanks


Thanks,
Sanjay


On Tue, Jun 22, 2010 at 6:52 PM, Mitch Skinner
<[hidden email]>  wrote:
   
In the future, JBrowse will probably use the autoindexing option as
suggested by that error message.

Right now, though, you can get around this by creating the index manually
with samtools; you'd write something like:

$ samtools index /var/www/jbrowse/docs/tutorial/data_files/20100311.bam

(using the full path to the samtools program if it's not in your path)

Mitch

On 06/22/2010 02:12 AM, sanjay shah wrote:
     
Hi,

I have a BAM file   and when i execute the following command  to
convert the BAM to Json :

$$ bin/flatfile-to-json.pl  --bam
/var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon
--tracklabel BAM_data --key "BAM Data"

I get the following error;

No index file for
/var/www/jbrowse/docs/tutorial/data_files/20100311.bam; try opening
file with -autoindex at /usr/local/lib/perl/5.10.0/Bio/DB/Sam.pm line
1940

I have installed the  prerequisite installed for browsing BAM files in
Jbrowse .I also have  the corresponding reference file in Json  and am
able to browse in Jbrowse.


Do we have to create any index for browsing BAM files in Jbrowse
before we convert it to Json .Please help  me in resolving the
following error.



Thanks,
Sanjay


       

     


--
Success is how many times u smile each day every day.

   


 




--
Success is how many times u smile each day every day.


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Re: Error converting BAM to JSON for browsing in Jbrowse

sanjay shah
Hi Mitch,

Thanks,

Regards,
Sanjay



On Fri, Jul 2, 2010 at 6:47 PM, Mitch Skinner <[hidden email]> wrote:
Yes.  It's a bug, I'm aware of it, and I'm working on it, just like all the other bugs and shortcomings in JBrowse.  You've encountered the frontier of active JBrowse development, on the development branch.

Mitch


On 07/02/2010 12:01 AM, sanjay shah wrote:
Hi Mitch,

Thanks .But do that error really hampers the functionality of BAM files being visualized in Jbrowse(I mean is there any data ,information loss  due to this  in BAM to JSON conversion and visualization in Jbrowse.



Thanks,
Sanjay

On Thu, Jul 1, 2010 at 8:12 PM, Mitch Skinner <[hidden email]> wrote:
Hi,

I've seen this but I haven't yet figured out exactly what's going on.  I think it has something to do with paired-end reads, and it might be caused by reads whose pair-mate isn't mapped.

Handling paired-end reads better is something I'm currently working on.

Mitch


On 06/23/2010 01:35 AM, sanjay shah wrote:
Hi ,


Sorry Typo error in the earlier mail ..

   The bam file is "20100311.sorted.bam"  and not "20100311.bam"
that is being provided in the command after index has been created  as
:
  " 20100311.sorted.bam.bai ."..
So the command  executed is :
 $$ bin/flatfile-to-json.pl  --bam
  /var/www/jbrowse/docs/tutorial/data_files20100311.sorted.bam --cssclass exon
  --tracklabel BAM_data --key "BAM Data"


 which   throws the  following error

Use of uninitialized value in int at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25.
Use of uninitialized value in int at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25.
Use of uninitialized value in int at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25.
Use of uninitialized value in int at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25.
Use of uninitialized value in int at
/var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27.


please help ..Thanks

Thanks,
Sanjay




Thanks,
Sanjay

On Wed, Jun 23, 2010 at 2:10 PM, sanjay shah<[hidden email]>  wrote:
 
Hi ,

Thanks.I  did sort  the alignments and  then  created index manually
with samtools( I  have "20100311.sorted.bam.bai " file ) ; now when I
again try to convert BAM to JSON by issuing command as:


 $$ bin/flatfile-to-json.pl  --bam
 /var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon
 --tracklabel BAM_data --key "BAM Data"


I get  following error:

Use of uninitialized value in int at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25.
Use of uninitialized value in int at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25.
Use of uninitialized value in int at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25.
Use of uninitialized value in int at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27.
Use of uninitialized value in subtraction (-) at
/var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25.



Please help on this aspect ..Thanks


Thanks,
Sanjay


On Tue, Jun 22, 2010 at 6:52 PM, Mitch Skinner
<[hidden email]>  wrote:
   
In the future, JBrowse will probably use the autoindexing option as
suggested by that error message.

Right now, though, you can get around this by creating the index manually
with samtools; you'd write something like:

$ samtools index /var/www/jbrowse/docs/tutorial/data_files/20100311.bam

(using the full path to the samtools program if it's not in your path)

Mitch

On 06/22/2010 02:12 AM, sanjay shah wrote:
     
Hi,

I have a BAM file   and when i execute the following command  to
convert the BAM to Json :

$$ bin/flatfile-to-json.pl  --bam
/var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon
--tracklabel BAM_data --key "BAM Data"

I get the following error;

No index file for
/var/www/jbrowse/docs/tutorial/data_files/20100311.bam; try opening
file with -autoindex at /usr/local/lib/perl/5.10.0/Bio/DB/Sam.pm line
1940

I have installed the  prerequisite installed for browsing BAM files in
Jbrowse .I also have  the corresponding reference file in Json  and am
able to browse in Jbrowse.


Do we have to create any index for browsing BAM files in Jbrowse
before we convert it to Json .Please help  me in resolving the
following error.



Thanks,
Sanjay


       

     


--
Success is how many times u smile each day every day.

   


 




--
Success is how many times u smile each day every day.




--
Success is how many times u smile each day every day.

------------------------------------------------------------------------------
This SF.net email is sponsored by Sprint
What will you do first with EVO, the first 4G phone?
Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax