Missing name field in bedcov

[johnmu]

line:

cnvkit/cnvlib/coverage.py

Line 125 in 2d43983

chrom, start_s, end_s, name, basecount_s = line.split('\t')

samtools bedcov doesn't return a "name" fields as far as I know. Where does this name field come from?

[etal]

Sure it does, at least if the input BED file also contains a "name" field in the 4th column.

$ more some-targets.bed 
chr1    30330   30540   MIR1302-10
chr1    35051   35290   FAM138A
chr1    35290   35529   FAM138A
chr1    35623   35833   FAM138A
chr1    69039   69294   OR4F5
chr1    69294   69549   OR4F5
chr1    69549   69804   OR4F5
chr1    69804   70059   OR4F5
chr1    367618  367873  OR4F16
chr1    367873  368128  OR4F16

$ samtools bedcov -Q 1 some-targets.bed some-reads.bam 
chr1    30330   30540   MIR1302-10  0
chr1    35051   35290   FAM138A 0
chr1    35290   35529   FAM138A 50
chr1    35623   35833   FAM138A 0
chr1    69039   69294   OR4F5   0
chr1    69294   69549   OR4F5   1228
chr1    69549   69804   OR4F5   748
chr1    69804   70059   OR4F5   0
chr1    367618  367873  OR4F16  0
chr1    367873  368128  OR4F16  0


$ samtools 

Program: samtools (Tools for alignments in the SAM format)
Version: 0.1.19-44428cd
...

[johnmu]

Ah I see, yeah my BED file was missing the 4th column. Thanks!