error in editting binary file using sed command -


i trying remove lines in binary file(.bam) , make new 1 small example. tried sed command did not work , gave nothing. have this(when print using command : samtools view -h myfile.bam)

 @sq sn:5    ln:151834684  @sq sn:6    ln:149736546  @sq sn:7    ln:145441459  @sq sn:8    ln:129401213  @sq sn:9    ln:124595110  @sq sn:gl456210.1   ln:169725  @sq sn:gl456211.1   ln:241735  @sq sn:gl456212.1   ln:153618  @sq sn:gl456213.1   ln:39340  @sq sn:gl456216.1   ln:66673  @sq sn:mt   ln:16299  @sq sn:x    ln:171031299

and want this:

 @sq sn:5    ln:151834684  @sq sn:6    ln:149736546  @sq sn:7    ln:145441459  @sq sn:8    ln:129401213  @sq sn:9    ln:124595110  @sq sn:mt   ln:16299  @sq sn:x    ln:171031299

here command used:

samtools view -h accepted_hits.bam | sed -v 's/sn:gl456210.1/' |  samtools reheader - accepted_hits.bam > mybamfile.reheadered.bam

and when tried -e instead of -v gave error:

sed: -e expression #1, char 16: unterminated `s' command

do guys know how solve problem?


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