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@vmikkvmikk commented Jul 31, 2024

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Hello!

This PR adds a new feature to the seqkit sort command, allowing sequences to be sorted by their average Phred quality. The following options have been introduced:

  • -q or --by-avg-qual
  • --qual-ascii-base

With the implementation of quality estimation, I tried to follow the approach used in the fx2tab command.

However, the code currently won't work because the StringCount type (which was used for storing sequence length) cannot be used for storing average quality. Therefore, a new type (e.g., StringFloat), probably should be added to util/stringutil.

Could you please confirm that this is a useful feature and, if so, review the code?

PS. For the short ASCII base flag, -b is already occupied by --by-bases option, so it is not consistent with -b in fx2tab.

@shenwei356

shenwei356 commented Jul 31, 2024

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It looks good to me, thank you Vladimir! I'll handle the util package and merge this later.

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Add sorting by average quality to `seqkit sort` by vmikk · Pull Request #482 · shenwei356/seqkit · GitHub
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Hello!
This PR adds a new feature to the seqkit sort command, allowing sequences to be sorted by their average Phred quality. The following options have been introduced:
  • -q or --by-avg-qual
  • --qual-ascii-base
With the implementation of quality estimation, I tried to follow the approach used in the fx2tab command.
However, the code currently won't work because the StringCount type (which was used for storing sequence length) cannot be used for storing average quality. Therefore, a new type (e.g., StringFloat), probably should be added to util/stringutil.
Could you please confirm that this is a useful feature and, if so, review the code?
PS. For the short ASCII base flag, -b is already occupied by --by-bases option, so it is not consistent with -b in fx2tab.
@shenwei356
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It looks good to me, thank you Vladimir! I'll handle the util package and merge this later.
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Hello!
This PR adds a new feature to the seqkit sort command, allowing sequences to be sorted by their average Phred quality. The following options have been introduced:
  • -q or --by-avg-qual
  • --qual-ascii-base
With the implementation of quality estimation, I tried to follow the approach used in the fx2tab command.
However, the code currently won't work because the StringCount type (which was used for storing sequence length) cannot be used for storing average quality. Therefore, a new type (e.g., StringFloat), probably should be added to util/stringutil.
Could you please confirm that this is a useful feature and, if so, review the code?
PS. For the short ASCII base flag, -b is already occupied by --by-bases option, so it is not consistent with -b in fx2tab.
@shenwei356
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It looks good to me, thank you Vladimir! I'll handle the util package and merge this later.
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Add sorting by average quality to `seqkit sort` by vmikk · Pull Request #482 · shenwei356/seqkit · GitHub
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Hello!
This PR adds a new feature to the seqkit sort command, allowing sequences to be sorted by their average Phred quality. The following options have been introduced:
  • -q or --by-avg-qual
  • --qual-ascii-base
With the implementation of quality estimation, I tried to follow the approach used in the fx2tab command.
However, the code currently won't work because the StringCount type (which was used for storing sequence length) cannot be used for storing average quality. Therefore, a new type (e.g., StringFloat), probably should be added to util/stringutil.
Could you please confirm that this is a useful feature and, if so, review the code?
PS. For the short ASCII base flag, -b is already occupied by --by-bases option, so it is not consistent with -b in fx2tab.
@shenwei356
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It looks good to me, thank you Vladimir! I'll handle the util package and merge this later.
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Add sorting by average quality to `seqkit sort` by vmikk · Pull Request #482 · shenwei356/seqkit · GitHub
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Add sorting by average quality to seqkit sort - #482
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Hello!
This PR adds a new feature to the seqkit sort command, allowing sequences to be sorted by their average Phred quality. The following options have been introduced:
  • -q or --by-avg-qual
  • --qual-ascii-base
With the implementation of quality estimation, I tried to follow the approach used in the fx2tab command.
However, the code currently won't work because the StringCount type (which was used for storing sequence length) cannot be used for storing average quality. Therefore, a new type (e.g., StringFloat), probably should be added to util/stringutil.
Could you please confirm that this is a useful feature and, if so, review the code?
PS. For the short ASCII base flag, -b is already occupied by --by-bases option, so it is not consistent with -b in fx2tab.
@shenwei356
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It looks good to me, thank you Vladimir! I'll handle the util package and merge this later.
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var __m = "*";
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Add sorting by average quality to `seqkit sort` by vmikk · Pull Request #482 · shenwei356/seqkit · GitHub
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Hello!
This PR adds a new feature to the seqkit sort command, allowing sequences to be sorted by their average Phred quality. The following options have been introduced:
  • -q or --by-avg-qual
  • --qual-ascii-base
With the implementation of quality estimation, I tried to follow the approach used in the fx2tab command.
However, the code currently won't work because the StringCount type (which was used for storing sequence length) cannot be used for storing average quality. Therefore, a new type (e.g., StringFloat), probably should be added to util/stringutil.
Could you please confirm that this is a useful feature and, if so, review the code?
PS. For the short ASCII base flag, -b is already occupied by --by-bases option, so it is not consistent with -b in fx2tab.
@shenwei356
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It looks good to me, thank you Vladimir! I'll handle the util package and merge this later.
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Add sorting by average quality to `seqkit sort` by vmikk · Pull Request #482 · shenwei356/seqkit · GitHub
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Hello!
This PR adds a new feature to the seqkit sort command, allowing sequences to be sorted by their average Phred quality. The following options have been introduced:
  • -q or --by-avg-qual
  • --qual-ascii-base
With the implementation of quality estimation, I tried to follow the approach used in the fx2tab command.
However, the code currently won't work because the StringCount type (which was used for storing sequence length) cannot be used for storing average quality. Therefore, a new type (e.g., StringFloat), probably should be added to util/stringutil.
Could you please confirm that this is a useful feature and, if so, review the code?
PS. For the short ASCII base flag, -b is already occupied by --by-bases option, so it is not consistent with -b in fx2tab.
@shenwei356
shenwei356
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It looks good to me, thank you Vladimir! I'll handle the util package and merge this later.
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Add sorting by average quality to `seqkit sort` by vmikk · Pull Request #482 · shenwei356/seqkit · GitHub
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Add sorting by average quality to seqkit sort - #482
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Hello!
This PR adds a new feature to the seqkit sort command, allowing sequences to be sorted by their average Phred quality. The following options have been introduced:
  • -q or --by-avg-qual
  • --qual-ascii-base
With the implementation of quality estimation, I tried to follow the approach used in the fx2tab command.
However, the code currently won't work because the StringCount type (which was used for storing sequence length) cannot be used for storing average quality. Therefore, a new type (e.g., StringFloat), probably should be added to util/stringutil.
Could you please confirm that this is a useful feature and, if so, review the code?
PS. For the short ASCII base flag, -b is already occupied by --by-bases option, so it is not consistent with -b in fx2tab.
@shenwei356
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It looks good to me, thank you Vladimir! I'll handle the util package and merge this later.
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