What does “fetching by region is not available for SAM files” means?
$begingroup$
I am used to gzip/biopython solutions when dealing with sequencing data, but now I wish to switch to more elegant pysam. So I looked at the manual, but run into quite bizarre troubles with the first couple of lines using my bam file
import pysam
samfile = pysam.AlignmentFile("3_Tms_1_mapped.bam", "rb")
for read in samfile.fetch('3_Tms_b3v08_scaf000159'):
print(read)
samfile.close()
returns ValueError: fetching by region is not available for SAM files. Well, the file is bam. I tried to google the error but the only hits I found are the lines in the source code of pysam that check if the file is bam/cram or sam, so somehow pysam thinks that my bam is a sam. How can I convince him otherwise? I also have noticed that the manual is for python 2.7, that's maybe where the problem comes from...
If you wish to reproduce my problem, here is my bam file.
python bam pysam
asked 14 hours ago
Kamil S JaronKamil S Jaron
2,937742
$endgroup$
add a comment |
$begingroup$
I am used to gzip/biopython solutions when dealing with sequencing data, but now I wish to switch to more elegant pysam. So I looked at the manual, but run into quite bizarre troubles with the first couple of lines using my bam file
import pysam
samfile = pysam.AlignmentFile("3_Tms_1_mapped.bam", "rb")
for read in samfile.fetch('3_Tms_b3v08_scaf000159'):
print(read)
samfile.close()
returns ValueError: fetching by region is not available for SAM files. Well, the file is bam. I tried to google the error but the only hits I found are the lines in the source code of pysam that check if the file is bam/cram or sam, so somehow pysam thinks that my bam is a sam. How can I convince him otherwise? I also have noticed that the manual is for python 2.7, that's maybe where the problem comes from...
If you wish to reproduce my problem, here is my bam file.
python bam pysam
asked 14 hours ago
Kamil S JaronKamil S Jaron
2,937742
$endgroup$
add a comment |
$begingroup$
I am used to gzip/biopython solutions when dealing with sequencing data, but now I wish to switch to more elegant pysam. So I looked at the manual, but run into quite bizarre troubles with the first couple of lines using my bam file
import pysam
samfile = pysam.AlignmentFile("3_Tms_1_mapped.bam", "rb")
for read in samfile.fetch('3_Tms_b3v08_scaf000159'):
print(read)
samfile.close()
returns ValueError: fetching by region is not available for SAM files. Well, the file is bam. I tried to google the error but the only hits I found are the lines in the source code of pysam that check if the file is bam/cram or sam, so somehow pysam thinks that my bam is a sam. How can I convince him otherwise? I also have noticed that the manual is for python 2.7, that's maybe where the problem comes from...
If you wish to reproduce my problem, here is my bam file.
python bam pysam
asked 14 hours ago
Kamil S JaronKamil S Jaron
2,937742
$endgroup$
I am used to gzip/biopython solutions when dealing with sequencing data, but now I wish to switch to more elegant pysam. So I looked at the manual, but run into quite bizarre troubles with the first couple of lines using my bam file
import pysam
samfile = pysam.AlignmentFile("3_Tms_1_mapped.bam", "rb")
for read in samfile.fetch('3_Tms_b3v08_scaf000159'):
print(read)
samfile.close()
returns ValueError: fetching by region is not available for SAM files. Well, the file is bam. I tried to google the error but the only hits I found are the lines in the source code of pysam that check if the file is bam/cram or sam, so somehow pysam thinks that my bam is a sam. How can I convince him otherwise? I also have noticed that the manual is for python 2.7, that's maybe where the problem comes from...
If you wish to reproduce my problem, here is my bam file.
python bam pysam
python bam pysam
asked 14 hours ago
Kamil S JaronKamil S Jaron
2,937742
asked 14 hours ago
Kamil S JaronKamil S Jaron
2,937742
asked 14 hours ago
Kamil S JaronKamil S Jaron
2,937742
asked 14 hours ago
Kamil S JaronKamil S Jaron
2,937742
asked 14 hours ago
Kamil S JaronKamil S Jaron
2,937742
2,937742
add a comment |
add a comment |
2 Answers
2
active
oldest
votes
$begingroup$
You don't have the index file for the bam file you're using. I used this script on the file you linked to (changing the name so that it corresponds to the right file and a contig in that file):
#!/usr/bin/env python3
import pysam
samfile = pysam.AlignmentFile("3_Tce_1_mapped.bam", "rb")
for read in samfile.fetch('3_Tce_b3v08_scaf005149'):
print(read)
samfile.close()
The directory I ran it in had:
$ ls 3*
3_Tce_1_mapped.bam
And I got the error you described:
$ foo.py
Traceback (most recent call last):
File "/home/terdon/scripts/foo.py", line 5, in <module>
for read in samfile.fetch('3_Tce_b3v08_scaf005149'):
File "pysam/libcalignmentfile.pyx", line 1107, in pysam.libcalignmentfile.AlignmentFile.fetch
ValueError: fetching by region is not available for SAM files
However, indexing the bam file fixed it:
$ samtools sort 3_Tce_1_mapped.bam > 3_Tce_1_mapped.sorted.bam
$ mv 3_Tce_1_mapped.sorted.bam 3_Tce_1_mapped.bam
$ samtools index 3_Tce_1_mapped.bam
$ ls 3*
3_Tce_1_mapped.bam 3_Tce_1_mapped.bam.bai
$ foo.py | wc
227 2724 16725
So just sort and index your files before attempting to seek in them. Which makes sense since the index's job is primarily to allow seeking.
answered 14 hours ago
terdon♦terdon
4,7902830
$endgroup$
$begingroup$
I was thinking about indexing, but then I thought that if that would be the problem pysam would complain about sorting/indexing, not about file being sam. Do yo think it would be worth opening them a ticket to make the error message bit more meaningful?
$endgroup$
– Kamil S Jaron
12 hours ago
$begingroup$
Seeking, i.e. random access, requires an index. Note that this is not the only access pattern in pysam. You can access reads in a streaming fashion (for read in samfile:) without sorting, and you can access read pileups base-by-base (for column in samfile.pileup('chr1')), which does require an index if I understand correctly.
$endgroup$
– Daniel Standage
12 hours ago
$begingroup$
@KamilSJaron probably, yes. It obviously caused you some pain, and I'm sure you won't be alone. I only thought of this because I have seen similar cryptic errors and was wondering how it could seek without an index anyway.
$endgroup$
– terdon♦
12 hours ago
1
$begingroup$
@KamilSJaron Yes, I think it's an unhelpful error message, and it has caused me confusion in the past as well. If you open a ticket on Github I'd be happy to "pile on." :-)
$endgroup$
– Daniel Standage
12 hours ago
$begingroup$
@DanielStandage I am this close to suspending you for that horrible pun! I would too if I could stop chuckling for long enough!
$endgroup$
– terdon♦
12 hours ago
|
show 4 more comments
$begingroup$
Your 3_Tms_1_mapped.bam file, despite its filename extension, is in fact a bgzipped SAM file. You can verify this using htsfile, which is a small utility packaged with HTSlib:
$ htsfile 3_Tms_1_mapped.bam
3_Tms_1_mapped.bam: SAM version 1.3 BGZF-compressed sequence data
(For files that really are in BAM format, it reports BAM version 1 compressed sequence data.)
So the error message is accurate in this case.
answered 10 hours ago
John MarshallJohn Marshall
51326
$endgroup$
$begingroup$
Hmm, does it mean that this link is wrong? biopython.org/DIST/docs/api/Bio.bgzf-module.html I sort of thought that it's the same thing...
$endgroup$
– Kamil S Jaron
8 hours ago
$begingroup$
No. (Was there a particular part of that you think might be wrong?) But there is a difference between BGZF-compressing the plain text format, and a BAM file (whose decompressed underlying stream is a bespoke binary format that is different from the plain SAM text).
$endgroup$
– John Marshall
8 hours ago
add a comment |
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2 Answers
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active
oldest
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2 Answers
2
active
oldest
votes
active
oldest
votes
active
oldest
votes
$begingroup$
You don't have the index file for the bam file you're using. I used this script on the file you linked to (changing the name so that it corresponds to the right file and a contig in that file):
#!/usr/bin/env python3
import pysam
samfile = pysam.AlignmentFile("3_Tce_1_mapped.bam", "rb")
for read in samfile.fetch('3_Tce_b3v08_scaf005149'):
print(read)
samfile.close()
The directory I ran it in had:
$ ls 3*
3_Tce_1_mapped.bam
And I got the error you described:
$ foo.py
Traceback (most recent call last):
File "/home/terdon/scripts/foo.py", line 5, in <module>
for read in samfile.fetch('3_Tce_b3v08_scaf005149'):
File "pysam/libcalignmentfile.pyx", line 1107, in pysam.libcalignmentfile.AlignmentFile.fetch
ValueError: fetching by region is not available for SAM files
However, indexing the bam file fixed it:
$ samtools sort 3_Tce_1_mapped.bam > 3_Tce_1_mapped.sorted.bam
$ mv 3_Tce_1_mapped.sorted.bam 3_Tce_1_mapped.bam
$ samtools index 3_Tce_1_mapped.bam
$ ls 3*
3_Tce_1_mapped.bam 3_Tce_1_mapped.bam.bai
$ foo.py | wc
227 2724 16725
So just sort and index your files before attempting to seek in them. Which makes sense since the index's job is primarily to allow seeking.
answered 14 hours ago
terdon♦terdon
4,7902830
$endgroup$
$begingroup$
I was thinking about indexing, but then I thought that if that would be the problem pysam would complain about sorting/indexing, not about file being sam. Do yo think it would be worth opening them a ticket to make the error message bit more meaningful?
$endgroup$
– Kamil S Jaron
12 hours ago
$begingroup$
Seeking, i.e. random access, requires an index. Note that this is not the only access pattern in pysam. You can access reads in a streaming fashion (for read in samfile:) without sorting, and you can access read pileups base-by-base (for column in samfile.pileup('chr1')), which does require an index if I understand correctly.
$endgroup$
– Daniel Standage
12 hours ago
$begingroup$
@KamilSJaron probably, yes. It obviously caused you some pain, and I'm sure you won't be alone. I only thought of this because I have seen similar cryptic errors and was wondering how it could seek without an index anyway.
$endgroup$
– terdon♦
12 hours ago
1
$begingroup$
@KamilSJaron Yes, I think it's an unhelpful error message, and it has caused me confusion in the past as well. If you open a ticket on Github I'd be happy to "pile on." :-)
$endgroup$
– Daniel Standage
12 hours ago
$begingroup$
@DanielStandage I am this close to suspending you for that horrible pun! I would too if I could stop chuckling for long enough!
$endgroup$
– terdon♦
12 hours ago
|
show 4 more comments
$begingroup$
You don't have the index file for the bam file you're using. I used this script on the file you linked to (changing the name so that it corresponds to the right file and a contig in that file):
#!/usr/bin/env python3
import pysam
samfile = pysam.AlignmentFile("3_Tce_1_mapped.bam", "rb")
for read in samfile.fetch('3_Tce_b3v08_scaf005149'):
print(read)
samfile.close()
The directory I ran it in had:
$ ls 3*
3_Tce_1_mapped.bam
And I got the error you described:
$ foo.py
Traceback (most recent call last):
File "/home/terdon/scripts/foo.py", line 5, in <module>
for read in samfile.fetch('3_Tce_b3v08_scaf005149'):
File "pysam/libcalignmentfile.pyx", line 1107, in pysam.libcalignmentfile.AlignmentFile.fetch
ValueError: fetching by region is not available for SAM files
However, indexing the bam file fixed it:
$ samtools sort 3_Tce_1_mapped.bam > 3_Tce_1_mapped.sorted.bam
$ mv 3_Tce_1_mapped.sorted.bam 3_Tce_1_mapped.bam
$ samtools index 3_Tce_1_mapped.bam
$ ls 3*
3_Tce_1_mapped.bam 3_Tce_1_mapped.bam.bai
$ foo.py | wc
227 2724 16725
So just sort and index your files before attempting to seek in them. Which makes sense since the index's job is primarily to allow seeking.
answered 14 hours ago
terdon♦terdon
4,7902830
$endgroup$
$begingroup$
I was thinking about indexing, but then I thought that if that would be the problem pysam would complain about sorting/indexing, not about file being sam. Do yo think it would be worth opening them a ticket to make the error message bit more meaningful?
$endgroup$
– Kamil S Jaron
12 hours ago
$begingroup$
Seeking, i.e. random access, requires an index. Note that this is not the only access pattern in pysam. You can access reads in a streaming fashion (for read in samfile:) without sorting, and you can access read pileups base-by-base (for column in samfile.pileup('chr1')), which does require an index if I understand correctly.
$endgroup$
– Daniel Standage
12 hours ago
$begingroup$
@KamilSJaron probably, yes. It obviously caused you some pain, and I'm sure you won't be alone. I only thought of this because I have seen similar cryptic errors and was wondering how it could seek without an index anyway.
$endgroup$
– terdon♦
12 hours ago
1
$begingroup$
@KamilSJaron Yes, I think it's an unhelpful error message, and it has caused me confusion in the past as well. If you open a ticket on Github I'd be happy to "pile on." :-)
$endgroup$
– Daniel Standage
12 hours ago
$begingroup$
@DanielStandage I am this close to suspending you for that horrible pun! I would too if I could stop chuckling for long enough!
$endgroup$
– terdon♦
12 hours ago
|
show 4 more comments
$begingroup$
You don't have the index file for the bam file you're using. I used this script on the file you linked to (changing the name so that it corresponds to the right file and a contig in that file):
#!/usr/bin/env python3
import pysam
samfile = pysam.AlignmentFile("3_Tce_1_mapped.bam", "rb")
for read in samfile.fetch('3_Tce_b3v08_scaf005149'):
print(read)
samfile.close()
The directory I ran it in had:
$ ls 3*
3_Tce_1_mapped.bam
And I got the error you described:
$ foo.py
Traceback (most recent call last):
File "/home/terdon/scripts/foo.py", line 5, in <module>
for read in samfile.fetch('3_Tce_b3v08_scaf005149'):
File "pysam/libcalignmentfile.pyx", line 1107, in pysam.libcalignmentfile.AlignmentFile.fetch
ValueError: fetching by region is not available for SAM files
However, indexing the bam file fixed it:
$ samtools sort 3_Tce_1_mapped.bam > 3_Tce_1_mapped.sorted.bam
$ mv 3_Tce_1_mapped.sorted.bam 3_Tce_1_mapped.bam
$ samtools index 3_Tce_1_mapped.bam
$ ls 3*
3_Tce_1_mapped.bam 3_Tce_1_mapped.bam.bai
$ foo.py | wc
227 2724 16725
So just sort and index your files before attempting to seek in them. Which makes sense since the index's job is primarily to allow seeking.
answered 14 hours ago
terdon♦terdon
4,7902830
$endgroup$
You don't have the index file for the bam file you're using. I used this script on the file you linked to (changing the name so that it corresponds to the right file and a contig in that file):
#!/usr/bin/env python3
import pysam
samfile = pysam.AlignmentFile("3_Tce_1_mapped.bam", "rb")
for read in samfile.fetch('3_Tce_b3v08_scaf005149'):
print(read)
samfile.close()
The directory I ran it in had:
$ ls 3*
3_Tce_1_mapped.bam
And I got the error you described:
$ foo.py
Traceback (most recent call last):
File "/home/terdon/scripts/foo.py", line 5, in <module>
for read in samfile.fetch('3_Tce_b3v08_scaf005149'):
File "pysam/libcalignmentfile.pyx", line 1107, in pysam.libcalignmentfile.AlignmentFile.fetch
ValueError: fetching by region is not available for SAM files
However, indexing the bam file fixed it:
$ samtools sort 3_Tce_1_mapped.bam > 3_Tce_1_mapped.sorted.bam
$ mv 3_Tce_1_mapped.sorted.bam 3_Tce_1_mapped.bam
$ samtools index 3_Tce_1_mapped.bam
$ ls 3*
3_Tce_1_mapped.bam 3_Tce_1_mapped.bam.bai
$ foo.py | wc
227 2724 16725
So just sort and index your files before attempting to seek in them. Which makes sense since the index's job is primarily to allow seeking.
answered 14 hours ago
terdon♦terdon
4,7902830
answered 14 hours ago
terdon♦terdon
4,7902830
answered 14 hours ago
terdon♦terdon
4,7902830
answered 14 hours ago
terdon♦terdon
4,7902830
4,7902830
$begingroup$
I was thinking about indexing, but then I thought that if that would be the problem pysam would complain about sorting/indexing, not about file being sam. Do yo think it would be worth opening them a ticket to make the error message bit more meaningful?
$endgroup$
– Kamil S Jaron
12 hours ago
$begingroup$
Seeking, i.e. random access, requires an index. Note that this is not the only access pattern in pysam. You can access reads in a streaming fashion (for read in samfile:) without sorting, and you can access read pileups base-by-base (for column in samfile.pileup('chr1')), which does require an index if I understand correctly.
$endgroup$
– Daniel Standage
12 hours ago
$begingroup$
@KamilSJaron probably, yes. It obviously caused you some pain, and I'm sure you won't be alone. I only thought of this because I have seen similar cryptic errors and was wondering how it could seek without an index anyway.
$endgroup$
– terdon♦
12 hours ago
1
$begingroup$
@KamilSJaron Yes, I think it's an unhelpful error message, and it has caused me confusion in the past as well. If you open a ticket on Github I'd be happy to "pile on." :-)
$endgroup$
– Daniel Standage
12 hours ago
$begingroup$
@DanielStandage I am this close to suspending you for that horrible pun! I would too if I could stop chuckling for long enough!
$endgroup$
– terdon♦
12 hours ago
|
show 4 more comments
$begingroup$
I was thinking about indexing, but then I thought that if that would be the problem pysam would complain about sorting/indexing, not about file being sam. Do yo think it would be worth opening them a ticket to make the error message bit more meaningful?
$endgroup$
– Kamil S Jaron
12 hours ago
$begingroup$
Seeking, i.e. random access, requires an index. Note that this is not the only access pattern in pysam. You can access reads in a streaming fashion (for read in samfile:) without sorting, and you can access read pileups base-by-base (for column in samfile.pileup('chr1')), which does require an index if I understand correctly.
$endgroup$
– Daniel Standage
12 hours ago
$begingroup$
@KamilSJaron probably, yes. It obviously caused you some pain, and I'm sure you won't be alone. I only thought of this because I have seen similar cryptic errors and was wondering how it could seek without an index anyway.
$endgroup$
– terdon♦
12 hours ago
1
$begingroup$
@KamilSJaron Yes, I think it's an unhelpful error message, and it has caused me confusion in the past as well. If you open a ticket on Github I'd be happy to "pile on." :-)
$endgroup$
– Daniel Standage
12 hours ago
$begingroup$
@DanielStandage I am this close to suspending you for that horrible pun! I would too if I could stop chuckling for long enough!
$endgroup$
– terdon♦
12 hours ago
$begingroup$
I was thinking about indexing, but then I thought that if that would be the problem pysam would complain about sorting/indexing, not about file being sam. Do yo think it would be worth opening them a ticket to make the error message bit more meaningful?
$endgroup$
– Kamil S Jaron
12 hours ago
$begingroup$
I was thinking about indexing, but then I thought that if that would be the problem pysam would complain about sorting/indexing, not about file being sam. Do yo think it would be worth opening them a ticket to make the error message bit more meaningful?
$endgroup$
– Kamil S Jaron
12 hours ago
$begingroup$
Seeking, i.e. random access, requires an index. Note that this is not the only access pattern in pysam. You can access reads in a streaming fashion (
for read in samfile:) without sorting, and you can access read pileups base-by-base (for column in samfile.pileup('chr1')), which does require an index if I understand correctly.$endgroup$
– Daniel Standage
12 hours ago
$begingroup$
Seeking, i.e. random access, requires an index. Note that this is not the only access pattern in pysam. You can access reads in a streaming fashion (
for read in samfile:) without sorting, and you can access read pileups base-by-base (for column in samfile.pileup('chr1')), which does require an index if I understand correctly.$endgroup$
– Daniel Standage
12 hours ago
$begingroup$
@KamilSJaron probably, yes. It obviously caused you some pain, and I'm sure you won't be alone. I only thought of this because I have seen similar cryptic errors and was wondering how it could seek without an index anyway.
$endgroup$
– terdon♦
12 hours ago
$begingroup$
@KamilSJaron probably, yes. It obviously caused you some pain, and I'm sure you won't be alone. I only thought of this because I have seen similar cryptic errors and was wondering how it could seek without an index anyway.
$endgroup$
– terdon♦
12 hours ago
1
1
$begingroup$
@KamilSJaron Yes, I think it's an unhelpful error message, and it has caused me confusion in the past as well. If you open a ticket on Github I'd be happy to "pile on." :-)
$endgroup$
– Daniel Standage
12 hours ago
$begingroup$
@KamilSJaron Yes, I think it's an unhelpful error message, and it has caused me confusion in the past as well. If you open a ticket on Github I'd be happy to "pile on." :-)
$endgroup$
– Daniel Standage
12 hours ago
$begingroup$
@DanielStandage I am this close to suspending you for that horrible pun! I would too if I could stop chuckling for long enough!
$endgroup$
– terdon♦
12 hours ago
$begingroup$
@DanielStandage I am this close to suspending you for that horrible pun! I would too if I could stop chuckling for long enough!
$endgroup$
– terdon♦
12 hours ago
|
show 4 more comments
$begingroup$
Your 3_Tms_1_mapped.bam file, despite its filename extension, is in fact a bgzipped SAM file. You can verify this using htsfile, which is a small utility packaged with HTSlib:
$ htsfile 3_Tms_1_mapped.bam
3_Tms_1_mapped.bam: SAM version 1.3 BGZF-compressed sequence data
(For files that really are in BAM format, it reports BAM version 1 compressed sequence data.)
So the error message is accurate in this case.
answered 10 hours ago
John MarshallJohn Marshall
51326
$endgroup$
$begingroup$
Hmm, does it mean that this link is wrong? biopython.org/DIST/docs/api/Bio.bgzf-module.html I sort of thought that it's the same thing...
$endgroup$
– Kamil S Jaron
8 hours ago
$begingroup$
No. (Was there a particular part of that you think might be wrong?) But there is a difference between BGZF-compressing the plain text format, and a BAM file (whose decompressed underlying stream is a bespoke binary format that is different from the plain SAM text).
$endgroup$
– John Marshall
8 hours ago
add a comment |
$begingroup$
Your 3_Tms_1_mapped.bam file, despite its filename extension, is in fact a bgzipped SAM file. You can verify this using htsfile, which is a small utility packaged with HTSlib:
$ htsfile 3_Tms_1_mapped.bam
3_Tms_1_mapped.bam: SAM version 1.3 BGZF-compressed sequence data
(For files that really are in BAM format, it reports BAM version 1 compressed sequence data.)
So the error message is accurate in this case.
answered 10 hours ago
John MarshallJohn Marshall
51326
$endgroup$
$begingroup$
Hmm, does it mean that this link is wrong? biopython.org/DIST/docs/api/Bio.bgzf-module.html I sort of thought that it's the same thing...
$endgroup$
– Kamil S Jaron
8 hours ago
$begingroup$
No. (Was there a particular part of that you think might be wrong?) But there is a difference between BGZF-compressing the plain text format, and a BAM file (whose decompressed underlying stream is a bespoke binary format that is different from the plain SAM text).
$endgroup$
– John Marshall
8 hours ago
add a comment |
$begingroup$
Your 3_Tms_1_mapped.bam file, despite its filename extension, is in fact a bgzipped SAM file. You can verify this using htsfile, which is a small utility packaged with HTSlib:
$ htsfile 3_Tms_1_mapped.bam
3_Tms_1_mapped.bam: SAM version 1.3 BGZF-compressed sequence data
(For files that really are in BAM format, it reports BAM version 1 compressed sequence data.)
So the error message is accurate in this case.
answered 10 hours ago
John MarshallJohn Marshall
51326
$endgroup$
Your 3_Tms_1_mapped.bam file, despite its filename extension, is in fact a bgzipped SAM file. You can verify this using htsfile, which is a small utility packaged with HTSlib:
$ htsfile 3_Tms_1_mapped.bam
3_Tms_1_mapped.bam: SAM version 1.3 BGZF-compressed sequence data
(For files that really are in BAM format, it reports BAM version 1 compressed sequence data.)
So the error message is accurate in this case.
answered 10 hours ago
John MarshallJohn Marshall
51326
edited 12 mins ago
answered 10 hours ago
John MarshallJohn Marshall
51326
answered 10 hours ago
John MarshallJohn Marshall
51326
answered 10 hours ago
John MarshallJohn Marshall
51326
51326
$begingroup$
Hmm, does it mean that this link is wrong? biopython.org/DIST/docs/api/Bio.bgzf-module.html I sort of thought that it's the same thing...
$endgroup$
– Kamil S Jaron
8 hours ago
$begingroup$
No. (Was there a particular part of that you think might be wrong?) But there is a difference between BGZF-compressing the plain text format, and a BAM file (whose decompressed underlying stream is a bespoke binary format that is different from the plain SAM text).
$endgroup$
– John Marshall
8 hours ago
add a comment |
$begingroup$
Hmm, does it mean that this link is wrong? biopython.org/DIST/docs/api/Bio.bgzf-module.html I sort of thought that it's the same thing...
$endgroup$
– Kamil S Jaron
8 hours ago
$begingroup$
No. (Was there a particular part of that you think might be wrong?) But there is a difference between BGZF-compressing the plain text format, and a BAM file (whose decompressed underlying stream is a bespoke binary format that is different from the plain SAM text).
$endgroup$
– John Marshall
8 hours ago
$begingroup$
Hmm, does it mean that this link is wrong? biopython.org/DIST/docs/api/Bio.bgzf-module.html I sort of thought that it's the same thing...
$endgroup$
– Kamil S Jaron
8 hours ago
$begingroup$
Hmm, does it mean that this link is wrong? biopython.org/DIST/docs/api/Bio.bgzf-module.html I sort of thought that it's the same thing...
$endgroup$
– Kamil S Jaron
8 hours ago
$begingroup$
No. (Was there a particular part of that you think might be wrong?) But there is a difference between BGZF-compressing the plain text format, and a BAM file (whose decompressed underlying stream is a bespoke binary format that is different from the plain SAM text).
$endgroup$
– John Marshall
8 hours ago
$begingroup$
No. (Was there a particular part of that you think might be wrong?) But there is a difference between BGZF-compressing the plain text format, and a BAM file (whose decompressed underlying stream is a bespoke binary format that is different from the plain SAM text).
$endgroup$
– John Marshall
8 hours ago
add a comment |
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