Trouble with newRecord "undeclared identifier" in bam

[akkellogg]

Hi, I'm having trouble initiating new records based on an old Bam file. My goal is to make modifications to certain fields (i.e mapping quality) based on criteria within a record.

Since I can't modify the existing record directly, I figured I would generate new records with the desired modifications but maintain old fields from the original record. However, I keep running into an error when trying to compile. Below is the relevant code up to where the compilation fails:

import hts

var
   oaln: Bam

proc copy_most_fields(old_read: Record, old_bam: Bam): Record =
   var header = old_bam.hdr
   var new_read = newRecord(header)

The compilation error I receive is:

./hts_nim_static_builder -s src/my_script.nim -n my_script.nimble {"--debug": false, "--nim-src-file": src/my_script.nim, "": [], "--": false, "--nimble-file": my_script.nimble, "--tag": latest, "--deps": []} docker run -v /path/to/my/script/my_script:/path/to/my/script/my_script -v /path/to/my/script/my_script:/load/ brentp/musl-hts-nim:latest /usr/local/bin/nsb -n /path/to/my/script/my_script/my_script.nimble -s /path/to/my/script/my_script/src/my_script.nim -- -d:danger -d:release @["-n", "/path/to/my/script/my_script/my_script.nimble", "-s", "/path/to/my/script/my_script/src/my_script.nim", "--", "-d:danger", "-d:release"] {"": ["-d:danger", "-d:release"], "--nim-src-file": /path/to/my/script/my_script/src/my_script.nim, "--": true, "--deps": [], "--nimble-file": /path/to/my/script/my_script/my_script.nimble} Verifying dependencies for my_script@0.1.0 Info: Dependency on hts@any version already satisfied Verifying dependencies for hts@0.3.16 Hint: used config file '/nim/config/nim.cfg' [Conf] Hint: used config file '/nim/config/config.nims' [Conf] ......................... /path/to/my/script/my_script/src/my_script.nim(10, 22) Error: undeclared identifier: 'newRecord'

I am using the hts_nim_static_builder and I have hts-nim installed, so I'm not sure if this is user error or an issue with the function

[brentp]

Hi, you are using newRecord it must be NewRecord. nim is usually not case-sensitive for variable names, but the first letter matters.

[akkellogg]

Not sure how I missed that. I kept looking back and forth at the docs and didn't process that capital N.

Thanks!

[akkellogg]

Following up with another issue regarding this script. I'm no longer getting an error regarding creating the new record, however, I am having trouble filling in fields I want to copy from the original read:

proc copy_most_fields(old_read: Record, old_bam: Bam): Record =
  var header = old_bam.hdr
  var new_read = NewRecord(header)
  new_read.set_qname(old_read.qname())
  new_read.SamField.SAM_SEQ = old_read.SamField.SAM_SEQ
  new_read.SamField.SAM_FLAG = old_read.SamField.SAM_FLAG
  new_read.SamField.SAM_POS = old_read.SamField.SAM_POS
  new_read.SamField.SAM_CIGAR = old_read.SamField.SAM_CIGAR
  new_read.SamField.SAM_RNAME = old_read.SamField.SAM_RNAME
  new_read.SamField.SAM_RNEXT = old_read.SamField.SAM_RNEXT
  new_read.SamField.SAM_PNEXT = old_read.SamField.SAM_PNEXT
  new_read.SamField.SAM_TLEN = old_read.SamField.SAM_TLEN
  new_read.SamField.SAM_QUAL = old_read.SamField.SAM_QUAL
  new_read.isize = old_read.isize
  return new_read

But when I try to compile I get /path/to/my/script/my_script/src/my_script.nim(11, 11) Error: type mismatch: got <Record> but expected 'SamField = enum' which would pertain to the line new_read.SamField.SAM_SEQ = old_read.SamField.SAM_SEQ I'm not sure what is the best way to set fields in the new record

[brentp]

Hi, this is not how those fields work. SamField is an enum, not a property of a record.

I would use: var new_read = old_read.copy() and then modify the fields that need to be modified. `SamFields are mostly used as arguments to bam.set_option.

[akkellogg]

However, copying every field of the full read, means I can no longer update the mapping_quality field

I've tried:

proc copy_most_fields(old_read: Record, old_bam: Bam): Record =
  var header = old_bam.hdr
  var new_read = old_read.copy()
  new_read.mapping_quality = 60
  return new_read

which returns Error: attempting to call undeclared routine: 'mapping_quality='

and I've tried:

proc copy_most_fields(old_read: Record, old_bam: Bam): Record =
  var header = old_bam.hdr
  var new_read = old_read.copy()
  new_read.mapping_quality() = 60
  return new_read

which returns Error: 'mapping_quality(new_read)' cannot be assigned to

[brentp]

You can assign to the mapping quality directly with: new_read.b.core.qual = 60 as I haven't exposed a setter.

[akkellogg]

Thank you! Looks like it is working now